--- /dev/null
+ CLUSTER
+ Cluster analysis of UNRES simulation results
+ ---------------------------------------------
+
+TABLE OF CONTENTS
+-----------------
+
+1. License terms
+
+2. References
+
+3. Functions of the program
+
+4. Installation
+
+5. Running the program
+
+6. Input and output files
+ 6.1. Summary of files
+ 6.2. The main input file
+ 6.2.1. Title
+ 6.2.2. General data
+ 6.2.3. Energy-term weights and parameter files
+ 6.2.4 Molecule data
+ 6.2.4.1. Sequence information
+ 6.2.4.2. Dihedral angle restraint information
+ 6.2.4.3. Disulfide-bridge data
+ 6.2.5. Reference structure
+ 6.3. Main output file (out)
+ 6.4. Output coordinate files
+ 6.4.1. The internal coordinate (int) files
+ 6.4.2. The Cartesian coordinate (x) files
+ 6.4.3. The PDB files
+ 6.4.3.1. CLUST-UNRES runs
+ 6.4.3.2. CLUST-WHAM runs
+ 6.4.3.2.1. Conformation family files
+ 6.4.3.2.2. Average-structure file
+ 6.5. The conformation-distance file
+ 6.6. The clustering-tree PicTeX file
+
+7. Support
+
+1. LICENSE TERMS
+----------------
+
+* This software is provided free of charge to academic users, subject to the
+ condition that no part of it be sold or used otherwise for commercial
+ purposes, including, but not limited to its incorporation into commercial
+ software packages, without written consent from the authors. For permission
+ contact Prof. H. A. Scheraga, Cornell University.
+
+* This software package is provided on an "as is" basis. We in no way warrant
+ either this software or results it may produce.
+
+* Reports or publications using this software package must contain an
+ acknowledgment to the authors and the NIH Resource in the form commonly
+used
+ in academic research.
+
+2. REFERENCES
+-------------
+
+The program incorporates the hierarchical-clustering subroutine, hc.f written
+by G. Murtagh (refs 1 and 2). The subroutine contains seven methods of
+hierarchical clustering.
+
+[1] F. Murtagh. Multidimensional clustering algorithms; Physica-Verlag:
+ Vienna, Austria, 1985.
+[2] F. Murtagh, A. Heck. MultiVariate data analysis; Kluwer Academic:
+ Dordrecht, Holland, 1987.
+[3] A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, K. Wachucik,
+ H.A. Scheraga.
+ Modification and optimization of the united-residue (UNRES) potential
+ energy function for canonical simulations. I. Temperature dependence of the
+ effective energy function and tests of the optimization method with single
+ training proteins. J. Phys. Chem. B, 2007, 111, 260-285.
+[4] S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 2. Off-lattice tests of the method with single
+ proteins. J. Phys. Chem. B., 2004, 108, 16934-16949.
+
+3. FUNCTIONS OF THE PROGRAM
+---------------------------
+
+The program runs cluster analysis of UNRES simulation results. There are two
+versions of the program depending on the origin of input conformation:
+
+1) CLUST-UNRES: performs cluster analysis of conformations that are obtained
+ directly from UNRES runs (CSA, MCM, MD, (M)REMD, multiple-conformation
+ energy minimization). The source code and other important files are
+ deposited in CLUST-UNRES subdirectory
+
+ The source code of this version is deposited in clust-unres/src
+
+2) CLUST-WHAM: performs cluster analysis of conformations obtained in UNRES
+ MREMD simulations and then processed with WHAM (weighted histogram analysis
+ method). This enables the user to obtain clusters as conformational
+ ensembles at a given temperature and to compute their probabilities
+ (section 2.5 of ref 3). This version is deposited in the CLUST-WHAM
+ subdirectory. This version has single- and multichain variants, whose
+ source codes are deposited in the following subdirectories:
+
+ a) clust-wham/src single-chain proteins
+
+ b) clust-wham/src-M oligomeric proteins
+
+The version developed for oligomeric proteins treats whole system as a single
+chain with dummy residues inserted. It also works for single chains but is
+not fully checked and it is recommended to use single-chain version for
+single-chain proteins.
+
+4. INSTALLATION
+---------------
+
+Customize Makefile to your system. See section 7 of the description of UNRES
+for compiler flags that are used to created executables for a particular
+force field. There are already several Makefiles prepared for various
+systems and force fields.
+
+Run make in the appropriate source directory version. CLUST-UNRES runs
+only in single-processor mode an CLUST-WHAM runs in both serial and parallel
+mode [only conformation-distance (rmsd) calculations are parallelized].
+The parallel version uses MPI.
+
+5. RUNNING THE PROGRAM
+----------------------
+
+The program requires a parallel system to run. Depending on system,
+either the wham.csh C-shell script (in WHAM/bin directory) can be started
+using mpirun or the binary in the C-shell script must be executed through
+mpirun. See the wham.csh C-shell script and section 6 for the files
+processed by the program.
+
+6. INPUT AND OUTPUT FILES
+-------------------------
+
+6.1. SUMMARY OF THE FILES
+-------------------------
+
+The C-shell script wham.csh is used to run the program (see the
+bin/WHAM directory). The data files that the script needs are mostly the same as
+for UNRES (see section 6 of UNRES description). In addition, the environmental
+variable CONTFUN specifies the method to assess whether two side chains
+are at contact; if EONTFUN=GB, the criterion defined by eq 8 of ref 4 is
+used to assess whether two side chains are at contact. Also, the parameter
+files from the C-shell scripts are overridden if the data from Hamiltonian
+MREMD are processed; if so, the parameter files are defined in the main
+input file.
+
+The main input file must have inp extension. If it is INPUT.inp, the output
+files are as follows:
+
+Coordinate input file COORD.ext, where ext denotes file extension in one of the
+following formats:
+
+INT (extension int; UNRES angles theta, gamma, alpha, and beta),
+X (extension x; UNRES Cartesian coordinate format; from MD),
+PDB (extension pdb; Protein Data Bank format; fro MD),
+CX (extension cx; xdrf format; from WHAM).
+
+INPUT_clust.out (single-processor mode) or INPUT_clust.out_xxx (parallel mode) -
+ output file(s) (INPUT.out_000 is the main output file for parallel mode).
+
+COORD_clust.int: leading (lowest-energy) members of the families
+ in internal-coordinate format.
+COORD_clust.x: leading members of the families in UNRES Cartesian coordinate
+ format.
+COORD_xxxx.pdb or COORD_xxxx_yyy.pdb (CLUST-UNRES): PDB file of member yyy
+ of family xxxx; yyy is omitted if the family contains only one member
+ within a given energy cut-off.
+COORD_TxxxK_yyyy.pdb: concatenated conformations in PDB format of the
+ members of family yyyy clustered at T=xxxK ranked by probabilities in
+ descending order at this temperature (CLUST-WHAM).
+COORD_T_xxxK_ave.pdb: cluster-averaged coordinates and coordinates of a
+ member of each family that is closest to the cluster average in PDB
+ format, concatenated in a single file (CLUST-WHAM).
+
+INPUT_clust.tex: PicTeX code of the cluster tree.
+
+INPUT.rms: rmsds between conformations.
+
+6.2. MAIN INPUT FILE
+--------------------
+
+This file has the same structure as the UNRES input file; most of the data are
+input in a keyword-based form (see section 7.1 of UNRES description). The data
+are grouped into records, referred to as lines. Each record, except for the
+records that are input in non-keyword based form, can be continued by placing
+an ampersand (&) in column 80. Such a format is referred to as the data list
+format.
+
+In the following description, the default values are given in parentheses.
+
+6.2.1. Title (80-character string)
+----------------------------------
+
+6.2.2. General data (data list format)
+--------------------------------------
+
+NRES (0) - the number of residues
+
+ONE_LETTER - if present, the sequence is input in one-letter code.
+
+SYM (1) - number of chains with same sequence (for oligomeric proteins only),
+
+WITH_DIHED_CONSTR - if present, dihedral-angle restraints were imposed in the
+ processed MREMD simulations
+
+RESCALE (1) - Choice of the type of temperature dependence of the force field.
+0 - no temperature dependence
+1 - homographic dependence (not implemented yet with any force field)
+2 - hyperbolic tangent dependence [3].
+
+DISTCHAINMAX (50.0) - for oligomeric proteins, distance between the chains
+ above which restraints will be switched on to keep the chains at a
+ reasonable distance.
+
+PDBOUT - clusters will be printed in PDB format.
+
+ECUT - energy cut-off criterion to print conformations (UNRES-CLUST runs).
+ Only those families will be output the energy of the lowest-energy
+ conformation of which is within ECUT kcal/mol above that of the
+ lowest-energy conformation and for a family only those members will be
+ output which have energy within ECUT kcal/mol above the energy of the
+ lowest-energy member of the family.
+
+PRINT_CART - output leading members of the families in UNRES x format.
+
+PRINT_INT - output leading members of the families in UNRES int format.
+
+REF_STR - if present, reference structure is input and rmsd will be computed
+ with respect to it (CLUST-UNRES only; rmsd is provided in the cx file
+ from WHAM for CLUST-WHAM runs).
+
+PDBREF - if present, reference structure will be read in from a pdb file.
+
+SIDE - side chains will be considered in superposition when calculating rmsd
+
+CA_ONLY - only the Calpha atoms will be used in rmsd calculation
+
+NSTART (0) - first residue to superpose
+
+NEND (0) - last residue to superpose
+
+NTEMP (1) - number of temperatures at which probabilities will be calculated
+ and clustering performed (CLUST-WHAM)
+
+TEMPER (NTEMP tiles) - temperatures at which clustering will be performed
+ (CLUST-WHAM)
+
+EFREE - if present, conformation entropy factor is read if the conformation
+ is input from an x or pdb file
+
+PROB (0.99) - cut-off on the summary probability of the conformations that
+ are clustered at a given temperature (CLUST-WHAM)
+
+IOPT (2) - clustering algorithm:
+
+1 - Ward's minimum variance method
+2 - single link method
+3 - complete link method
+4 - average link (or group average) method
+5 - McQuitty's method
+6 - Median (Gower's) method
+7 - centroid method
+
+Instead of IOPT=1, MINTREE and instead of IOPT=2 MINVAR can be specified
+
+NCUT (1) - number of cut-offs in clustering
+
+CUTOFF (-1.0; NCUT values) cut-offs at which clustering will be performed;
+ at the cut-off flagged by a "-" sign clustering will be performed with
+ cutoff value=abs(cutoff(i)) and conformations corresponding to clusters
+ will be output in the desired format.
+
+MAKE_TREE - if present, produce a clustering-tree graph
+
+PLOT_TREE - if present, the tree is written in PicTeX format to a file
+
+PRINT_DIST - if present, distance (rmsd) matrix is printed to main output
+ file
+PUNCH_DIST - if present, the upper-triangle of the distance matrix will be
+ printed to a file
+
+6.2.3. Energy-term weights and parameter files
+----------------------------------------------
+
+WSC (1.0) - side-chain-side-chain interaction energy
+
+WSCP (1.0) - side chain-peptide group interaction energy
+
+WELEC (1.0) - peptide-group-peptide group interaction energy
+
+WEL_LOC (1.0)- third-order backbone-local correlation energy
+
+WCORR (1.0) - fourth-order backbone-local correlation energy
+
+WCORR5 (1.0) - fifth-order backbone-local correlation energy
+
+WCORR6 (1.0) - sixth-order backbone-local correlation energy
+
+WTURN3 (1.0) - third-order backbone-local correlation energy of pairs of
+ peptide groups separated by a single peptide group
+
+WTURN4 (1.0) - fourth-order backbone-local correlation energy of pairs of
+ peptide groups separated by two peptide groups
+
+WTURN6 (1.0) - sixth-order backbone-local correlation energy for pairs of
+ peptide groups separated by four peptide groups
+
+WBOND (1.0) - virtual-bond-stretching energy
+
+WANG (1.0) - virtual-bond-angle-bending energy
+
+WTOR (1.0) - virtual-bond-torsional energy
+
+WTORD (1.0) - virtual-bond-double-torsional energy
+
+WSCCOR (1.0) - sequence-specific virtual-bond-torsional energy
+
+WDIHC (0.0) - dihedral-angle-restraint energy
+
+WHPB (1.0) - distance-restraint energy
+
+SCAL14 (0.4) - scaling factor of 1,4-interactions
+
+6.2.4. Molecule information
+-----------------------------
+
+6.2.4.1. Sequence information
+-----------------------------
+
+Amino-acid sequence
+
+3-letter code: Sequence is input in format 20(1X,A3)
+
+1-letter code: Sequence is input in format 80A1
+
+6.2.4.2. Dihedral angle restraint information
+---------------------------------------------
+
+This is the information about dihedral-angle restraints, if any are present.
+It is specified only when WITH_DIHED_CONSTR is present in the first record.
+
+1st line: ndih_constr - number of restraints (free format)
+
+2nd line: ftors - force constant (free format)
+
+Each of the following ndih_constr lines:
+
+idih_constr(i),phi0(i),drange(i) (free format)
+
+idih_constr(i) - the number of the dihedral angle gamma corresponding to the
+ith restraint
+
+phi0(i) - center of dihedral-angle restraint
+
+drange(i) - range of flat well (no restraints for phi0(i) +/- drange(i))
+
+6.2.4.3. Disulfide-bridge data
+------------------------------
+
+1st line: NS, (ISS(I),I=1,NS) (free format)
+
+NS - number of cystine residues forming disulfide bridges
+
+ISS(I) - the number of the Ith disulfide-bonding cystine in the sequence
+
+2nd line: NSS, (IHPB(I),JHPB(I),I=1,NSS) (free format)
+
+NSS - number of disulfide bridges
+
+IHPB(I),JHPB(I) - the first and the second residue of ith disulfide link
+
+Because the input is in free format, each line can be split
+
+6.2.5. Reference structure
+--------------------------
+
+If PDBREF is specified, filename with reference (experimental) structure,
+otherwise UNRES internal coordinates as the theta, gamma, alpha, and beta
+angles.
+
+6.3. Main output file (out)
+------------------------------------------------
+
+The main (with name INPUT_clust.out or INPUT_clust.out_000 for parallel runs)
+output file contains the results of clustering (numbers of families
+at different cut-off values, probabilities of clusters, composition of
+families, and rmsd values corresponding to families (0 if rmsd was not
+computed or read from WHAM-generated cx file).
+
+The output files corresponding to non-master processors
+(INPUT_clust.out_xxx where xxx>0 contain only the information up to the
+clustering protocol. These files can be deleted right after the run.
+
+Excerpts from the a sample output file are given below:
+
+CLUST-UNRES:
+
+THERE ARE 20 FAMILIES OF CONFORMATIONS
+
+FAMILY 1 CONTAINS 2 CONFORMATION(S):
+ 42 -2.9384E+03 50 -2.9134E+03
+
+
+Max. distance in the family: 14.0; average distance in the family: 14.0
+
+FAMILY 2 CONTAINS 3 CONFORMATION(S):
+ 13 -2.9342E+03 7 -2.8827E+03 10 -2.8682E+03
+
+CLUST-WHAM:
+
+AT CUTOFF: 200.00000
+Maximum distance found: 137.82
+Free energies and probabilities of clusters at 325.0 K
+clust efree prob sumprob
+ 1 -76.5 0.25035 0.25035
+ 2 -76.5 0.24449 0.49484
+ 3 -76.4 0.21645 0.71129
+ 4 -76.4 0.20045 0.91174
+ 5 -75.8 0.08826 1.00000
+
+
+THERE ARE 5 FAMILIES OF CONFORMATIONS
+
+FAMILY 1 WITH TOTAL FREE ENERGY -7.65228E+01 CONTAINS 548 CONFORMATION(S):
+8363 -7.332E+013939 -7.332E+012583 -7.332E+017395 -7.332E+019932 -7.332E+01
+5816 -7.332E+013096 -7.332E+012663 -7.332E+014099 -7.332E+016822 -7.332E+01
+3176 -7.332E+017542 -7.332E+018933 -7.332E+017315 -7.332E+01 200 -7.332E+01.
+.
+5637 -7.062E+018060 -7.061E+013797 -7.060E+018800 -7.057E+016295 -7.057E+01
+6298 -7.057E+012332 -7.057E+012709 -7.057E+01
+
+Max. distance in the family: 16.5; average distance in the family: 8.8
+Average RMSD 8.22 A
+
+6.4. Output coordinate files
+----------------------------
+
+6.4.1. The internal coordinate (int) files
+------------------------------------------
+
+The file with name COORD_clust.int contains the angles theta, gamma, alpha,
+and beta of all residues of the leaders (lowest UNRES energy conformations
+from consecutive families for CLUST-UNRES runs and lowest free energy
+conformations for CLUST-WHAM runs). The format is the same as that of the
+file output by UNRES; see section 9.1.1 of UNRES description.
+
+For CLUST-WHAM runs, the first line contains more items:
+
+number of family (format i5)
+UNRES free energy of the conformation (format f12.3)
+Free energy of the entire family (format f12.3)
+number of disulfide bonds (format i2)
+list disulfide-bonded pairs (format 2i3)
+conformation class number (0 if not provided) (format i10)
+
+6.4.2. The Cartesian coordinate (x) files
+-----------------------------------------
+
+The file with name COORD_clust.x contains the Cartesian coordinates of the
+alpha-carbon and side-chain-center coordinates. The coordinate format is
+as in section 9.1.2 of UNRES description and the first line contains the
+following items:
+
+Number of the family (format I5)
+UNRES free energy of the conformation (format f12.3)
+Free energy of the entire family (format f12.3)
+number of disulfide bonds (format i2)
+list disulfide-bonded pairs (format 2i3)
+conformation class number (0 if not provided) (format i10)
+
+6.4.3. The PDB files
+--------------------
+
+The PDB files are in standard format (see
+ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf).
+The ATOM records contain Calpha coordinates (CA) or UNRES side-chain-center
+coordinates (CB). For oligomeric proteins chain identifiers are present
+(A, B, ..., etc.) and each chain ends with a TER record. Coordinates of a
+single conformation or multiple conformations The header (REMARK) records
+and the contents depends on cluster run type. The next subsections are devoted
+to different run types.
+
+6.4.3.1. CLUST-UNRES runs
+---------------------------
+
+The files contain the members of the families obtained from clustering such
+that the lowest-energy conformation of a family is within ECUT kcal/mol higher
+in energy than the lowest-energy conformation. Again, within a family, only
+those conformations are output whose energy is within ECUT kcal/mol above
+that of the lowest-energy member of the family. Families and the members
+of a family within a family are ranked by increasing energy. The file names are:
+
+COORD_xxxx.pdb where xxxx is the number of the family, if the family contains
+ only one member of if only one member is output.
+
+COORD_xxxx_yyy.pdb where xxxx is the number of the family and yyy is the number
+ of the member of this family.
+
+An example is the following:
+
+REMARK R0001 ENERGY -2.93843E+03
+ATOM 1 CA GLY 1 0.000 0.000 0.000
+ATOM 2 CA HIS 2 3.800 0.000 0.000
+ATOM 3 CB HIS 2 5.113 1.656 0.015
+ATOM 4 CA VAL 3 5.927 -3.149 0.000
+.
+.
+.
+ATOM 346 CB GLU 183 -43.669 -32.853 -7.320
+TER
+CONECT 1 2
+CONECT 2 4 3
+.
+.
+.
+CONECT 341 343 342
+CONECT 343 344
+CONECT 345 346
+
+where ENERGY is the UNRES energy. The CONECT records defined the Calpha-Calpha
+and Calpha-SC connection.
+
+6.4.3.2. CLUST-WHAM runs
+--------------------------
+
+The program generates a file for each family with its members and a summary
+file with ensemble-averaged conformations for all families. These are described
+in the two next sections.
+
+6.4.3.2.1. Conformation family files
+------------------------------------
+
+For each family, the file name is COORD_TxxxK_yyyy.pdb, where yyyy is the
+number of the family and xxx is the integer part of the temperature (K).
+The first REMARK line in the file contains the information about the free
+energy and average rmsd of the entire cluster and, for each conformation,
+the initial REMARK line contains these quantities for this conformation.
+Same applies to oligomeric proteins, for which the TER records separate the
+chains and the ENDMDL record separates conformations.
+An example is given below.
+
+REMARK CLUSTER 1 FREE ENERGY -7.65228E+01 AVE RMSD 8.22
+REMARK 1BDD L18G full clust ENERGY -7.33241E+01 RMS 10.40
+ATOM 1 CA VAL 1 18.059 -33.585 4.616 1.00 5.00
+ATOM 2 CB VAL 1 18.720 -32.797 3.592 1.00 5.00
+.
+.
+.
+ATOM 115 CA LYS 58 29.641 -44.596 -8.159 1.00 5.00
+ATOM 116 CB LYS 58 27.593 -45.927 -8.930 1.00 5.00
+TER
+CONECT 1 3 2
+CONECT 3 5 4
+.
+.
+CONECT 113 114
+CONECT 115 116
+TER
+REMARK 1BDD L18G full clust ENERGY -7.33240E+01 RMS 10.04
+ATOM 1 CA VAL 1 3.174 2.833 -34.386 1.00 5.00
+ATOM 2 CB VAL 1 3.887 2.811 -33.168 1.00 5.00
+.
+.
+ATOM 115 CA LYS 58 16.682 6.695 -20.438 1.00 5.00
+ATOM 116 CB LYS 58 18.925 5.540 -20.776 1.00 5.00
+TER
+CONECT 1 3 2
+CONECT 3 5 4
+CONECT 113 114
+CONECT 115 116
+TER
+
+6.4.3.2.2. Average-structure file
+---------------------------------
+
+The file name is COORD_T_xxxK_ave.pdb. The entries are in pairs; the first
+one is cluster-averaged conformation and the second is a family member which
+has the lowest rmsd from this average conformation. Computing average
+conformations is explained in section 2.5 of ref 3. Example excerpts from
+an entry corresponding to a given family are shown below. The last
+number in each ATOM record is the rmsd of the mean coordinate of a given
+atom averaged over the cluster.
+
+REMAR AVERAGE CONFORMATIONS AT TEMPERATURE 300.00
+REMARK CLUSTER 1
+REMARK 2HEP clustering 300K ENERGY -8.22572E+01 RMS 3.29
+ATOM 1 CA MET 1 -17.748 48.148 -19.284 1.00 5.96
+ATOM 2 CB MET 1 -17.373 47.911 -19.294 1.00 6.34
+ATOM 3 CA ILE 2 -18.770 49.138 -18.133 1.00 3.98
+.
+.
+.
+ATOM 80 CB PHE 41 -14.353 44.680 -15.642 1.00 2.62
+ATOM 81 CA ARG 42 -11.619 41.645 -13.117 1.00 4.06
+ATOM 82 CB ARG 42 -11.330 40.378 -13.313 1.00 5.19
+TER
+CONECT 1 3 2
+CONECT 3 5 4
+.
+.
+.
+CONECT 76 78 77
+CONECT 78 79
+CONECT 79 80
+CONECT 81 82
+TER
+REMARK 2HEP clustering 300K ENERGY -8.22572E+01 RMS 3.29
+ATOM 1 CA MET 1 -37.698 40.489 -32.408 1.00 5.96
+ATOM 2 CB MET 1 -38.477 39.426 -34.159 1.00 6.34
+.
+.
+.
+ATOM 80 CB PHE 41 -35.345 50.342 -31.371 1.00 2.62
+ATOM 81 CA ARG 42 -33.603 54.332 -27.130 1.00 4.06
+ATOM 82 CB ARG 42 -33.832 53.074 -24.415 1.00 5.19
+TER
+CONECT 1 3 2
+CONECT 3 5 4
+.
+.
+.
+CONECT 76 78 77
+CONECT 78 79
+CONECT 79 80
+CONECT 81 82
+TER
+
+
+6.5. The conformation-distance file
+-----------------------------------
+
+The file name is INPUT_clust.rms. It contains the upper-diagonal part of
+the matrix of rmsds between conformations and differences between their
+energies:
+
+i,j,rmsd,energy(j)-energy(i) (format 2i5,2f10.5)
+
+where i and j, j>i are the numbers of the conformations, rmsd is the rmsd
+between conformation i and conformation j and energy(i) and energy(j) are
+the UNRES energies of conformations i and j, respectively.
+
+6.6. The clustering-tree PicTeX file
+------------------------------------
+
+This file contains the PicTeX code of the clustering tree. The file name is
+INPUT_clust.tex. It should be supplemented with LaTeX preamble and final
+commands or incorporated into a LaTeX source and compiled with LaTeX. The
+picture is produced by running LaTeX followed by dvips, dvipdf or other command
+to convert LaTeX-generated dvi files into a human-readable files.
+
+7. SUPPORT
+----------
+
+ Dr. Adam Liwo
+ Faculty of Chemistry, University of Gdansk
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.
+ phone: +48 58 523 5430
+ fax: +48 58 523 5472
+ e-mail: adam@chem.univ.gda.pl
+
+ Dr. Cezary Czaplewski
+ Faculty of Chemistry, University of Gdansk
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.
+ phone: +48 58 523 5430
+ fax: +48 58 523 5472
+ e-mail: czarek@chem.univ.gda.pl
+
+Prepared by Adam Liwo, 02/19/12
--- /dev/null
+ ----------------
+ UNRESPACK v. 3.0
+ ----------------
+
+A package to run united-residue protein simulations with the UNRES force field.
+It is a successor of earlier more specific version of UNRES to predict
+protein structure by global optimization (v. 1.0) and of the molecular dynamics
+version (version 2.0).
+
+LICENSE TERMS
+-------------
+
+* This software is provided free of charge to academic users, subject to the
+ condition that no part of it be sold or used otherwise for commercial
+ purposes, including, but not limited to its incorporation into commercial
+ software packages, without written consent from the authors. For permission
+ contact Prof. H. A. Scheraga, Cornell University.
+
+* This software package is provided on an "as is" basis. We in no way warrant
+ either this software or results it may produce.
+
+* Reports or publications using this software package must contain an
+ acknowledgment to the authors and the NIH Resource in the form commonly used
+ in academic research.
+
+The package has the following directory structure
+
+unrespack-v.3.0
+ |
+ |---------doc (documentation)
+ |
+ |---------PARAM (force field parameters)
+ |
+ |---------source
+ | |
+ | |-----unres (UNRES source codes; various versions)
+ | | |
+ | | |---src_MIN (only energy evaluation and minimization)
+ | | |---src_CSA (all functions except MD, includes CSA)
+ | | |---src_MD (all functions except CSA, includes MD, single chains)
+ | | |---src_MD-M (all functions except CSA, includes MD, oligomeric proteins)
+ | |-----wham (weighted analysis method source codes)
+ | | |
+ | | |---src (single chains)
+ | | |---src-M (oligomeric proteins)
+ | |
+ | |-----cluster (cluster analysis source coded)
+ | | |
+ | | |---clust-unres
+ | | | |
+ | | | |----src (input data from UNRES)
+ | | |
+ | | |---clust-wham (input data from WHAM)
+ | | |
+ | | |----src (for single-chain proteins)
+ | | |----src-M (for oligomeric proteins)
+ | |
+ | |-----xdrfpdb (file format conversion source codes)
+ | |
+ | |---src (single chains)
+ | |---src-M (oligomers)
+ |
+ |----------bin (C-shell script, batch scripts, and pre-compiled binaries)
+ | |
+ | |-----unres
+ | | |
+ | | |---CSA
+ | | |---MD
+ | |
+ | |-----wham
+ | |-----cluster
+ | |-----xdrfpdb
+ |
+ |--------examples
+ |
+ |-----unres
+ |-----wham
+ |-----cluster
+
+The distribution files and directories are the following:
+
+unrespack-v.3.0.tar.gz - gzipped tarfile of the entire package, with directory
+ structure as above.
+
+unres-src-v.3.0.tar.gz - UNRES source codes; uncompresses to give the directories
+ with UNRES source codes (src_CSA, src_MD, src_MD-M)
+
+wham-src-v.3.0.tar.gz - WHAM source codes; uncompresses to give the directories
+ with WHAM source codes (src and src-M)
+
+cluster-src-v.3.0.tar.gz - CLUSTER source codes; uncompresses to give the
+ diresctories with CLUSTER source codes (clust-unres/src, clust-wham/src
+ and clust-wham/src-M)
+
+xdrfpdb-v.3.0.tar.gz - XDRFPBD source codes; uncompresses to give the xdrfpdb
+ directory
+
+unrespack-bin-v.3.0.tar.gz - UNRES binaries; uncompresses to give the bin
+ directory and subdirectories with the elements of the package.
+
+unrespack-examples-v.3.0.tar.gz - examples; uncompresses to give the examples
+ directory and subdirectories.
+
+PARAM.tar.gz - force field parameters; uncompresses to give PARAM directory
+
+unrespack-doc-v.3.0.tar.gz - all documentation; uncompresses to give the doc
+ directory.
+
+To uncompress a tar-gz file of a package say:
+
+gzip -cd package.tar.gz | tar xf -
+
+Each directory contains a READMRE file to explain its contents.
+
+CREDITS TO DEVELOPERS OF CODES IMPORTED INTO UNRES
+--------------------------------------------------
+
+All programs use the fitsq subroutine written by Dr. Kenneth D. Gibson,
+Cornell University, retired.
+
+The MD program uses the surfatom subroutine written by Dr. J.W. Ponder,
+Washington University.
+
+The SUMSL subroutine (Gay, Assoc. Comput. Math. Trans. Math. Software, 9,
+503-524, 1983, is used for minimization.
+
+The CLUSTER program uses the hc subroutine developed by Dr. G. Murtagh,
+ESA/ESO/STECF, Garching.
+
+UNRES, WHAM, CLUSTER, and XDRFPDB use the Europort Data Library (xdrf) developed
+by Dr. F. van Hoesel, Groeningen University, to write and read compressed data
+files.
--- /dev/null
+ UNRES - A PROGRAM FOR COARSE-GRAINED SIMULATIONS OF PROTEINS
+ ------------------------------------------------------------
+
+TABLE OF CONTENTS
+-----------------
+
+1. License terms
+
+2. Credits
+
+3. General information
+ 3.1. Purpose
+ 3.2. Functions of the program
+ 3.2. Companion programs
+ 3.4. Programming language
+ 3.5. References
+
+4. Installation
+
+5. Customizing your batch and C-shell script
+
+6. Command line and files
+
+7. Force fields
+
+8. Input files
+ 8.1. Main input data file
+ 8.1.1. Title
+ 8.1.2. Control data (data list format; READ_CONTROL subroutine)
+ 8.1.2.1 Keywords to chose calculation type
+ 8.1.2.2 Specification of protein and structure output in non-MD
+ applications
+ 8.1.2.3. Miscellaneous
+ 8.1.3. Minimizer options (data list, subroutine READ_MINIM)
+ 8.1.4. CSA control parameters
+ 8.1.5. MCM data (data list, subroutine MCMREAD)
+ 8.1.6. MD data (subroutine READ_MDPAR)
+ 8.1.7. REMD/MREMD data (subroutine READ_REMDPAR)
+ 8.1.8. Energy-term weights (data list; subroutine MOLREAD)
+ 8.1.9. Input and/or reference PDB file name (text format; subroutine MOLREAD)
+ 8.1.10. Amino-acid sequence (free and text format)
+ 8.1.11. Disulfide-bridge information (free format; subroutine READ_BRIDGE)
+ 8.1.12. Dihedral-angle restraint data (free format; subroutine MOLREAD)
+ 8.1.13. Distance restraints (subroutine READ_DIST_CONSTR)
+ 8.1.14. Internal coordinates of the reference structure (free format;
+ subroutine READ_ANGLES)
+ 8.1.15. Internal coordinates of the initial conformation (free format;
+ subroutine READ_ANGLES)
+ 8.1.15.1. File name with internal coordinates of the conformations
+ to be processed
+ 8.1.16 Control data for energy map construction (data lists;
+ subroutine MAP_READ)
+ 8.2. Parameter files
+ 8.3. Input coordinate files
+ 8.4. Other input files
+
+9. Output files
+ 9.1. Coordinate files
+ 9.1.1. The internal coordinate (INT) files
+ 9.1.2. The plain Cartesian coordinate (X) files
+ 9.1.3. The compressed Cartesian coordinate (CX) files
+ 9.1.4. The Brookhaven Protein Data Bank format (PDB) files
+ 9.1.5. The SYBYLL (MOL2) files
+ 9.2. The summary (STAT) file
+ 9.2.1. Non-MD runs
+ 8.2.2. MD and MREMD runs
+ 9.3. CSA-specific output files
+
+10. Technical support contact information
+
+1. LICENSE TERMS
+----------------
+
+* This software is provided free of charge to academic users, subject to the
+ condition that no part of it be sold or used otherwise for commercial
+ purposes, including, but not limited to its incorporation into commercial
+ software packages, without written consent from the authors. For permission
+ contact Prof. H. A. Scheraga, Cornell University.
+
+* This software package is provided on an "as is" basis. We in no way warrant
+ either this software or results it may produce.
+
+* Reports or publications using this software package must contain an
+ acknowledgment to the authors and the NIH Resource in the form commonly used
+ in academic research.
+
+2. CREDITS
+----------
+
+The current and former developers of UNRES are listed in this section in alphabetic
+order together with their current or former affiliations.
+
+Maurizio Chinchio (formerly Cornell Univ., USA)
+Cezary Czaplewski (Univ. of Gdansk, Poland)
+Carlo Guardiani (Georgia State Univ., USA)
+Yi He (Cornell Univ., USA)
+Justyna Iwaszkiewicz (Swiss Institute of Bioinformatics, Switzerland)
+Dawid Jagiela (Univ. of Gdansk, Poland)
+Stanislaw Jaworski (deceased)
+Sebastian Kalinowski (Univ. of Gdansk, Poland)
+Urszula Kozlowska (deceased)
+Rajmund Kazmierkiewicz (Univ. of Gdansk, Poland)
+Jooyoung Lee (Korea Institute for Advanced Studies, Korea)
+Adam Liwo (Univ. of Gdansk, Poland)
+Mariusz Makowski (Univ. of Gdansk, Poland)
+Marian Nanias (formerly Cornell Univ., USA)
+Stanislaw Oldziej (Univ. of Gdansk, Poland)
+Jaroslaw Pillardy (Cornell Univ., USA)
+Daniel Ripoll (formerly Cornell Univ., USA)
+Jeff Saunders (Schrodinger Inc., USA)
+Harold A. Scheraga (Cornell Univ., USA)
+Hujun Shen (Dalian Institute of Chemical Physics, P.R. China)
+Adam Sieradzan (Univ. of Gdansk, Poland)
+Ryszard Wawak (formerly Cornell Univ., USA)
+Bartlomiej Zaborowski (Univ. of Gdansk, Poland)
+
+3. GENERAL INFORMATION
+----------------------
+
+3.1. Purpose
+------------
+
+Run coarse-grained calculations of polypeptide chains with the UNRES force field.
+There are two versions of the package which should be kept separate because of
+non-overlapping functions: version which runs global optimization (Conformational
+Space Annealing, CSA) and version that runs coarse-grained molecular dynamics and
+its extension. Because the installation, input file preparation and running CSA
+and MD versions are similar, a common manual is provided. Items specific
+for the CSA and MD version are marked "CSA" and "MD", respectively.
+
+MD version can be used to run multiple-chain proteins (however, that version of
+the code is a new release and might fail if yet un-checked functions are used).
+The multi-chain CSA version for this purpose is another package (written largely in
+C++).
+
+3.2. Functions of the program
+-----------------------------
+
+1. Perform energy evaluation of a single or multiple conformations
+ (serial and parallel) (CSA and MD)
+
+2. Run canonical mesoscopic molecular dynamics (serial and parallel) (MD).
+
+3. Run replica exchange (REMD) and multiplexing replica exchange (MREMD)
+ dynamics (parallel only) (MD).
+
+4. Run multicanonical molecular dynamics (parallel only) (MD).
+
+5. Run energy minimization (serial and parallel) (CSA and MD).
+
+6. Run conformational space annealing (CSA search) (parallel only) (CSA).
+
+7. Run Monte Carlo plus Minimization (MCM) (parallel only) (CSA).
+
+8. Run conformational family Monte Carlo (CFMC) calculations (CSA).
+
+9. Thread the sequence against a database from the PDB and minimize energy of
+ each structure (CSA).
+
+Energy and force evaluation is parallelized in MD version.
+
+3.3. Companion programs
+-----------------------
+
+The structures produced by UNRES can be used as inputs to the following programs provided
+with this package or separately:
+
+xdrf2pdb - converts the compressed coordinate files from MD (but not MREMD)runs into
+ PDB format.
+
+xdrf2pdb-m - same for MREMD runs (multiple trajectory capacity).
+
+xdrf2x - converts the plain Cartesian coordinate files into PDB format.
+
+WHAM - processes the coordinate files from MREMD runs and computes temperature profiles
+ of ensemble averages and computes the probabilities of conformations at selected
+ temperatures; also prepares data for CLUSTER and ZSCORE.
+
+CLUSTER - does the cluster analysis of the conformations; for MREMD runs takes the
+ coordinate files from WHAM which contain information to compute probabilities
+ of conformations at any temperature.
+
+PHOENIX - conversion of UNRES conformations to all-atom conformations.
+
+ZSCORE - force field optimization (for developers).
+
+Please consult the manuals of the corresponding packages for details. Note that not
+all of these packages are released yet; they will be released depending on their
+readiness for distribution. Contact Adam Liwo, Cezary Czaplewski or Stanislaw Oldziej
+for developmental versions of these programs.
+
+3.4. Programming language
+-------------------------
+
+This version of UNRES is written almost exclusively in Fortran 77; some subroutines
+for data management are in ansi-C. The package was parallelized with MPI.
+
+3.5. References
+---------------
+
+Citing the following references in your work that makes use of UNRES is gratefully
+acknowledged:
+
+[1] A. Liwo, S. Oldziej, M.R. Pincus, R.J. Wawak, S. Rackovsky, H.A. Scheraga.
+ A united-residue force field for off-lattice protein-structure simulations.
+ I: Functional forms and parameters of long-range side-chain interaction potentials
+ from protein crystal data. J. Comput. Chem., 1997, 18, 849-873.
+
+[2] A. Liwo, M.R. Pincus, R.J. Wawak, S. Rackovsky, S. Oldziej, H.A. Scheraga.
+ A united-residue force field for off-lattice protein-structure simulations.
+ II: Parameterization of local interactions and determination
+ of the weights of energy terms by Z-score optimization.
+ J. Comput. Chem., 1997, 18, 874-887.
+
+[3] A. Liwo, R. Kazmierkiewicz, C. Czaplewski, M. Groth, S. Oldziej, R.J. Wawak,
+ S. Rackovsky, M.R. Pincus, H.A. Scheraga.
+ United-residue force field for off-lattice protein-structure simulations.
+ III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials.
+ J. Comput. Chem., 1998, 19, 259-276.
+
+[4] A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Cumulant-based expressions for the multibody terms for the correlation between
+ local and electrostatic interactions in the united-residue force field.
+ J. Chem. Phys., 2001, 115, 2323-2347.
+
+[5] J. Lee, D.R. Ripoll, C. Czaplewski, J. Pillardy, W.J. Wedemeyer, H.A. Scheraga,
+ Optimization of parameters in macromolecular potential energy functions by
+ conformational space annealing. J. Phys. Chem. B, 2001, 105, 7291-7298
+
+[6] J. Pillardy, C. Czaplewski, A. Liwo, W.J. Wedemeyer, J. Lee, D.R. Ripoll,
+ P. Arlukowicz, S. Oldziej, Y.A. Arnautova, H.A. Scheraga,
+ Development of physics-based energy functions that predict medium-resolution
+ structures for proteins of the alpha, beta, and alpha/beta structural classes.
+ J. Phys. Chem. B, 2001, 105, 7299-7311
+
+[7] A. Liwo, P. Arlukowicz, C. Czaplewski, S. Oldziej, J. Pillardy, H.A. Scheraga.
+ A method for optimizing potential-energy functions by a hierarchical design
+ of the potential-energy landscape: Application to the UNRES force field.
+ Proc. Natl. Acad. Sci. U.S.A., 2002, 99, 1937-1942.
+
+[8] J. A. Saunders and H.A. Scheraga.
+ Ab initio structure prediction of two $\alpha$-helical oligomers
+ with a multiple-chain united-residue force field and global search.
+ Biopolymers, 2003, 68, 300-317.
+
+[9] J.A. Saunders and H.A. Scheraga.
+ Challenges in structure prediction of oligomeric proteins at the united-residue
+ level: searching the multiple-chain energy landscape with CSA and CFMC procedures.
+ Biopolymers, 2003, 68, 318-332.
+
+[10] S. Oldziej, U. Kozlowska, A. Liwo, H.A. Scheraga.
+ Determination of the potentials of mean force for rotation about Calpha-Calpha
+ virtual bonds in polypeptides from the ab initio energy surfaces of terminally
+ blocked glycine, alanine, and proline. J. Phys. Chem. A, 2003, 107, 8035-8046.
+
+[11] A. Liwo, S. Oldziej, C. Czaplewski, U. Kozlowska, H.A. Scheraga.
+ Parameterization of backbone-electrostatic and multibody contributions
+ to the UNRES force field for protein-structure prediction from ab initio
+ energy surfaces of model systems. J. Phys. A, 2004, 108, 9421-9438.
+
+[12] S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 2. Off-lattice tests of the method with single
+ proteins. J. Phys. Chem. B., 2004, 108, 16934-16949.
+
+[13] S. Oldziej, J. Lagiewka, A. Liwo, C. Czaplewski, M. Chinchio,
+ M. Nanias, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 3. Use of many proteins in optimization.
+ J. Phys. Chem. B., 2004, 108, 16950-16959.
+
+[14] M. Khalili, A. Liwo, F. Rakowski, P. Grochowski, H.A. Scheraga.
+ Molecular dynamics with the united-residue model of polypeptide chains.
+ I. Lagrange equations of motion and tests of numerical stability in the
+ microcanonical mode, J. Phys. Chem. B, 2005, 109, 13785-13797.
+
+[15] M. Khalili, A. Liwo, A. Jagielska, H.A. Scheraga.
+ Molecular dynamics with the united-residue model of polypeptide chains.
+ II. Langevin and Berendsen-bath dynamics and tests on model $\alpha$-helical
+ systems. J. Phys. Chem. B, 2005, 109, 13798-13810.
+
+[16] A. Liwo, M. Khalili, H.A. Scheraga.
+ Ab initio simulations of protein-folding pathways by molecular dynamics with
+ the united-residue model of polypeptide chains.
+ Proc. Natl. Acad. Sci. U.S.A., 2005, 102, 2362-2367.
+
+[17] F. Rakowski, P. Grochowski, B. Lesyng, A. Liwo, H. A. Scheraga.
+ Implementation of a symplectic multiple-time-step molecular dynamics algorithm,
+ based on the united-residue mesoscopic potential energy function.
+ J. Chem. Phys., 2006, 125, 204107.
+
+[18] M. Nanias, C. Czaplewski, H.A. Scheraga.
+ Replica exchange and multicanonical algorithms with the coarse-grained
+ united-residue (UNRES) force field.
+ J. Chem. Theory and Comput., 2006, 2, 513-528.
+
+[19] A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, K. Wachucik,
+ H.A. Scheraga.
+ Modification and optimization of the united-residue (UNRES) potential energy
+ function for canonical simulations. I. Temperature dependence of the effective
+ energy function and tests of the optimization method with single training
+ proteins.
+ J. Phys. Chem. B, 2007, 111, 260-285.
+
+[20] U. Kozlowska, A. Liwo, H.A. Scheraga.
+ Determination of virtual-bond-angle potentials of mean force for coarse-grained
+ simulations of protein structure and folding from ab initio energy surfaces of
+ terminally-blocked glycine, alanine, and proline.
+ J. Phys.: Condens. Matter, 2007, 19, 285203.
+
+[21] M. Chinchio, C. Czaplewski, A. Liwo, S. Oldziej, H.A. Scheraga.
+ Dynamic formation and breaking of disulfide bonds in molecular dynamics
+ simulations with the UNRES force field.
+ J. Chem. Theory and Comput., 2007, 3, 1236-1248.
+
+[22] A.V. Rojas, A. Liwo, H.A. Scheraga.
+ Molecular dynamics with the united-residue force field: Ab Initio folding
+ simulations of multichain proteins.
+ J. Phys. Chem. B, 2007, 111, 293-309.
+
+[23] A. Liwo, C. Czaplewski, S. Oldziej, A.V. Rojas, R. Kazmierkiewicz,
+ M. Makowski, R.K. Murarka, H.A. Scheraga.
+ Simulation of protein structure and dynamics with the coarse-grained UNRES
+ force field. In: Coarse-Graining of Condensed Phase and Biomolecular
+ Systems., ed. G. Voth, Taylor & Francis, 2008, Chapter 8, pp. 107-122.
+
+[24] C. Czaplewski, S. Kalinowski, A. Liwo, H.A. Scheraga.
+ Application of multiplexed replica exchange molecular dynamics
+ to the UNRES force field: tests with $\alpha$ and $\alpha+\beta$ proteins.
+ J. Chem. Theor. Comput., 2009, 5, 627-640.
+
+[24] Y. He, Y. Xiao, A. Liwo, H.A. Scheraga.
+ Exploring the parameter space of the coarse-grained UNRES force field by random
+ search: selecting a transferable medium-resolution force field.
+ J. Comput. Chem., 2009, 30, 2127-2135.
+
+[25] U. Kozlowska, A. Liwo. H.A. Scheraga.
+ Determination of side-chain-rotamer and side-chain and backbone
+ virtual-bond-stretching potentials of mean force from AM1 energy surfaces of
+ terminally-blocked amino-acid residues, for coarse-grained simulations of
+ protein structure and folding. 1. The Method.
+ J. Comput. Chem., 2010, 31, 1143-1153.
+
+[26] U. Kozlowska, G.G. Maisuradze, A. Liwo, H.A. Scheraga.
+ Determination of side-chain-rotamer and side-chain and backbone
+ virtual-bond-stretching potentials of mean force from AM1 energy surfaces of
+ terminally-blocked amino-acid residues, for coarse-grained simulations of
+ protein structure and folding. 2. Results, comparison with statistical
+ potentials, and implementation in the UNRES force field.
+ J. Comput. Chem., 2010, 31, 1154-1167.
+
+[27] A. Liwo, S. Oldziej, C. Czaplewski, D.S. Kleinerman, P. Blood, H.A. Scheraga.
+ Implementation of molecular dynamics and its extensions with the coarse-grained
+ UNRES force field on massively parallel systems; towards millisecond-scale
+ simulations of protein structure, dynamics, and thermodynamics.
+ J. Chem. Theor. Comput., 2010, 6, 890-909.
+
+4. INSTALLATION
+---------------
+
+The distribution is contained in the UNRES.tar.gz file. To uncompress say:
+
+gzip -cd UNRES.tar.gz | tar xf -
+
+This will produce a directory named UNRES with the following subdirectories:
+
+src_CSA - the CSA-version source directory.
+
+src_MD - the MD-version source directory, single chains.
+
+src_MD-M - the MD-version source directory, oligomeric proteins
+
+bin - the binaries/scripts directory; its BATCH_SCRIPTS directory contains the
+ batch scripts (at present the only example is for PBS: unres_3P_PBS.csh,
+ which is an UNRES calling script and start.mat, which is the batch script
+ submitted to the PBS system).
+
+doc - documentation (this file and EXAMPLES.TXT)
+
+examples - sample input files (see EXAMPLES.TXT for description).
+
+To produce the executable do the following:
+
+a) To build parallel version, make sure that MPI is installed in your system.
+ Note that the package will have limited functions when compiled in a single-CPU mode.
+ On linux cluster the command source $HOME/.env should be added to .tcshrc
+ or equivalent file to use parallel version of the program, the
+ alternative is to use queuing system like PBS.
+ In some cases the FORTRAN library subroutine GETENV does not work properly
+ with MPI, if the script is run interactively. In such a case try to
+ add the source mygentenv.F and turn on the -DMYGETENV preprocessor flag.
+
+b) Change directory to the respective source directory.
+
+c) Edit the appropriate Makefile (parallel program that includes CSA
+ procedure, the serial version is no longer supported, for serial task
+ parallel program can be run using only one processor) to customize to your
+ system. Makefiles for the following systems are provided:
+
+ Makefile_osf_f90 - OSF1/Tru64 UNIX HP Alphaserver with f90 compiler,
+ Makefile_lnx_pgf90 - Linux, the pgf90 compiler,
+ Makefile_lnx_ifc - Linux, ifc compiler.
+ Makefile_win_pgf90 - Windows, the pgf90 compiler.
+
+ Other systems should not cause problems; all you have to do is to change
+ the compiler, compiler options, and preprocessor options. Also, change the
+ BIN variable, if you want to put your binaries in other place than
+ PROTARCH/BIN. In the case of Makefile make sure that the MPI directories are
+ correctly specified.
+
+ The following architectures are defined in the .F source files:
+
+ AIX - AIX systems (put -DAIX as one of the preprocessor options, if
+ this is your system)
+
+ LINUX - Linux (put -DLINUX)
+
+ G77 - Gnu-Fortran compilers (might require sum moderate source code editing)
+ (put -DG77). The recommended compiler is gfortran and not g77.
+
+ PGI - PGI compilers
+
+ WINPGI - additional setting for PGI compilers for MS Windows
+
+ SGI - all SGI platforms; should also be good for SUN platforms (put -DSGI)
+
+ WIN - MS Windows with Digital Fortran compiler (put -DWIN)
+
+ For other platforms, the only problems might appear in connection with
+ machine-specific I/O instructions. Many files are opened in the append
+ mode, whose specification in the OPEN statement is quite machine-dependent.
+ In this case you might need to modify the source code accordingly.
+ The other platform dependent routines are the timing routines contained
+ in timing.F. In addition to the platforms specified above, ES9000, SUN,
+ KSR, and CRAY are defined there.
+
+ For parallel build -DMP and -DMPI must be set (these are set in Makefile).
+
+ IMPORTANT! Apart from this, two define flags: -DCRYST_TOR and -DMOMENT
+ define earlier versions of the force field. The MUST NOT be entered, if
+ the CASP5 and later versions of the force field are used.
+
+d) Build the unres executables by typing at your UNIX prompt:
+
+ make # will build unres
+
+ make clean # will remove the object files
+
+ The bin directory contains pre-built binaries for Red Hat Linux. These
+ executables are specified in the csh scripts listed in section 4.
+
+e) Customize the C-shell scripts unres.unres (to run the parallel version on
+ set of workstation). See the next section of this manual for guidance.
+
+After the executables are build and C-shell scripts customized, you can run the
+test examples contained in UNRES/examples.
+
+5. CUSTOMIZING YOUR C-SHELL SCRIPT
+----------------------------------
+
+IMPORTANT NOTE - The unres.csh script is for Linux and should also be easily
+adaptable to other systems running MPICH. This script is for interactive
+parallel jobs. Examples of scripts compatible with PBS (pbs.sub) and LoadLever
+(sp2.sub) queuing systems are also provided.
+
+Edit the following lines in your unres.csh script:
+
+set DD = your_database_directory
+
+e.g., if you installed the package on the directory /usr/local, this line
+looks like this:
+
+set DD = /usr/local/UNRES/PARAM
+
+set BIN = your_binaries_directory
+
+set FGPROCS = number_of_processors_per_energy/force_evaluation (MD)
+
+e.g., if the root directory is as above:
+
+set BIN = /usr/local/UNRES/bin
+
+6. COMMAND LINE AND FILES
+-------------------------
+
+To run UNRES interactively enter the following command at your Unix prompt
+or put it in the batch script:
+
+unres.csh POTENTIAL INPUT N_PROCS
+
+where:
+
+POTENTIAL specifies the side-chain interaction potential type and must be
+one of the following:
+
+LJ - 6-12 radial Lennard-Jones
+LJK - 6-12 radial Lennard-Jones-Kihara (shifted Lennard Jones)
+BP - 6-12 anisotropic Berne-Pechukas based on Gaussian overlap (dilated
+ Lennard-Jones)
+GB - 6-12 anisotropic Gay-Berne (shifted Lennard-Jones)
+GBV - 6-12 anisotropic Gay-Berne-Vorobjev (shifted Lennard-Jones)
+
+See section 4. (Force Fields) for explanation and usage.
+
+At present, only the LJ and GB potentials are applied. The LJ potential
+is used in the "CASP3" version of the UNRES force field that is able
+to predict only alpha-helical structures. All further version of the
+UNRES force field use the GB potential. For the description of all above-mentioned
+potentials see A. Liwo, St. Oldziej, M.R. Pincus, R.J. Wawak, S. Rackovsky,
+H.A. Scheraga, J. Comput. Chem., 1997, 18, 849-873.
+
+INPUT is the prefix for input and output files (see below)
+
+N_PROCS is the number of processors; for a CSA or REMD/MREMD run it MUST be at least 2.
+
+Note! The script takes one more variable, FGPROCS, as the fourth argument,
+which is the number of fine-grain processors to parallelize energy
+evaluations. The corresponding code is in UNRES/CSA, but it was written
+using MPL instead of MPI and therefore is never used in the present version.
+At present we have no plans to rewrite fine-grain parallelization using MPI,
+because we found that the scalability for up to 200 residue polypeptide
+chains was very poor, due to a small number of interactions and,
+correspondingly, unfavorable ratio of the overhead to the computation time.
+
+INPUT.inp contains the main input data and the control parameters of the CSA
+ method.
+
+INPUT.out_POTENTIAL_xxx - main output files from different processors; xxx
+ denotes the number of the processor
+
+INPUT_POTENTIALxxx.stat - summary files with the energies, energy components,
+ and RMS deviations of the conformations produced by each of the processors;
+ not used in CSA runs; also it outputs different quantity in MD/MREMD runs.
+
+CSA version specific files:
+
+INPUT_POTENTIALxxx.int - internal coordinates; in the CSA run
+ INPUT_POTENTIAL_000.int contains the coordinates of the conformations,
+ and the other files are empty
+
+INPUT.CSA.history - history file from a CSA run. This is an I/O file, because
+ it can be used to restart an interrupted CSA run.
+
+INPUT.CSA.seed - stores the random seed generated in a CSA run; written for
+ restart purposes.
+
+INPUT.CSA.bank - current bank of conformations obtained in CSA calculations
+ (expressed as internal coordinates). This information is also stored in
+ INPUT_POTENTIAL000.int
+
+INPUT.CSA.rbank - as above, but contains random-generated conformations.
+
+MD version specific files:
+
+INPUT_MDyyy.pdb - Cartesian coordinates of the conformations in PDB format.
+
+INPUT_MDyyy.x - Cartesian coordinates of the conformations in ASCII format.
+
+INPUT_MDyyy.cx - Cartesian coordinates of the conformations in compressed format
+ (need xdr2pdb to convert to PDB format).
+
+The program currently produces some more files, but they are not used
+for any purposes and most of them are scratched after a run is completed.
+
+The run script also contains definitions of the parameter files through the
+following environmental variables:
+
+SIDEPAR - parameters of the SC-SC interaction potentials (U_{SC SC});
+SCPPAR - parameters of the SC-p interaction potential (U_{SCp}); this file can
+ be ignored by specifying the -DOLDSCP preprocessor flag, which means that the
+ built-in parameters are used; at present they are the same as the parameters
+ in the file specified by SCPPAR;
+ELEPAR - parameters of the p-p interaction potentials (U_{pp});
+FOURIER - parameters of the multibody potentials of the coupling between the
+ backbone-local and backbone-electrostatic interactions (U_{corr});
+THETPAR - parameters of the virtual-bond-angle bending potentials (U_b);
+ROTPAR - parameters of the side-chain rotamer potentials (U_{rot});
+TORPAR - parameters of the torsional potentials (U_{rot});
+TORDPAR - parameters of the double-torsional potentials.
+SCCORPAR - parameters of the supplementary torsional sequence-specific potentials
+ (not implemented yet).
+
+7. FORCE FIELDS
+---------------
+
+UNRES is being developed since 1997 and several versions of the force field
+were produced. The settings and references to these force fields are
+summarized below.
+
+Force fields for CSA version (can be used in MD but haven't been parameterized for this
+purpose).
+
+---------------------------------------------------------------------------------------
+ Additional SC-SC Example script Structural
+Force field compiler flags potential and executables classes covered References
+ (Linux; PGF90
+ and IFC)
+---------------------------------------------------------------------------------------
+
+CASP3 -DCRYST_TOR LJ unres_CASP3.csh only alpha [1-3]
+ -DCRYST_BOND unres_pgf90_cryst_tor.exe
+ -DCRYST_THETA unres_ifc6_cryst_tor.exe
+ -DCRYST_SC
+ -DMOMENT
+
+ALPHA -DMOMENT GB unres_CASP4.csh only alpha [4-6]
+ -DCRYST_BOND unres_pgf90_moment.exe
+ -DCRYST_THETA unres_ifc6_moment.exe
+ -DCRYST_SC
+
+BETA -DMOMENT GB unres_CASP4.csh only beta [4-6]
+ -DCRYST_BOND unres_pgf90_moment.exe
+ -DCRYST_THETA unres_ifc6_moment.exe
+ -DCRYST_SC
+
+ALPHABETA -DMOMENT GB unres_CASP4.csh all [4-6]
+ -DCRYST_BOND unres_pgf90_moment.exe
+ -DCRYST_THETA unres_ifc6_moment.exe
+ -DCRYST_SC
+
+CASP5 -DCRYST_BOND GB unres_CASP5.csh all [7,8,11]
+ -DCRYST_THETA unres_pgf90.exe
+ -DCRYST_SC unres_ifc6.exe
+
+3P -DCRYST_BOND GB unres_3P.csh all [12,13]
+ -DCRYST_THETA unres_pgf90.exe
+ -DCRYST_SC unres_ifc6.exe
+
+4P -DCRYST_BOND GB unees_4P.csh all [12,13]
+ -DCRYST_THETA unres_pgf90.exe
+ -DCRYST_SC unres_ifc6.exe
+---------------------------------------------------------------------------------------
+
+Force fields for MD version
+
+---------------------------------------------------------------------------------------
+ Additional SC-SC Example script Structural
+Force field compiler flags potential and executables classes covered References
+ (Linux; PGF90
+ and IFC)
+---------------------------------------------------------------------------------------
+
+GAB -DCRYST_BOND GB unres_GAB.csh mostly alpha [19]
+ -DCRYST_THETA
+ -DCRYST_SC
+
+E0G -DCRYST_BOND GB unres_E0G.csh mostly alpha [19]
+ -DCRYST_THET
+ -DCRYST_SC
+
+1L2Y_1LE1 none GB unres_ab.csh all [20,25-27]
+
+---------------------------------------------------------------------------------------
+
+The example scripts (the *.csh filed) contain all appropriate parameter files, while
+the energy-term weights are provided in the example input files listed in EXAMPLES.TXT
+(*.inp; see section 5. for description of the input files). However, it is user's
+responsibility to specify appropriate compiler flags. Note that a version WILL NOT work,
+if the force-field specific compiler flags are not set. The parameter files specified
+in the run script also must strictly correspond to the energy-term weights specified in
+the input file. The parameter files for specific force fields are also specified below
+and the energy-term weights are specified in section 5.
+
+The parameter files are as follows (the environment variables from section 3 are
+used to identify the parameters):
+
+CASP3:
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_cryst.parm
+TORDPAR torsion_double_631Gdp.parm (not used)
+SIDEPAR scinter_LJ.parm
+ELEPAR electr.parm
+SCPPAR scp.parm
+FOURIER fourier_GAP.parm (not used)
+SCCORPAR rotcorr_AM1.parm (not used)
+
+ALPHA, BETA, ALPHABETA (CASP4):
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_ecepp.parm
+TORDPAR torsion_double_631Gdp.parm (not used)
+SIDEPAR scinter_GB.parm
+ELEPAR electr.parm
+SCPPAR scp.parm
+FOURIER fourier_GAP.parm
+SCCORPAR rotcorr_AM1.parm (not used)
+
+CASP5:
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_631Gdp.parm
+TORDPAR torsion_double_631Gdp.parm
+SIDEPAR scinter_GB.parm
+ELEPAR electr_631Gdp.parm
+SCPPAR scp.parm
+FOURIER fourier_opt.parm.1igd_iter7n_c
+SCCORPAR rotcorr_AM1.parm (not used)
+
+3P:
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_631Gdp.parm
+TORDPAR torsion_double_631Gdp.parm
+SIDEPAR sc_GB_opt.3P7_iter81_1r
+ELEPAR electr_631Gdp.parm
+SCPPAR scp.parm
+FOURIER fourier_opt.parm.1igd_hc_iter3_3
+SCCORPAR rotcorr_AM1.parm (not used)
+
+4P:
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_631Gdp.parm
+TORDPAR torsion_double_631Gdp.parm
+SIDEPAR sc_GB_opt.4P5_iter33_3r
+ELEPAR electr_631Gdp.parm
+SCPPAR scp.parm
+FOURIER fourier_opt.parm.1igd_hc_iter3_3
+SCCORPAR rotcorr_AM1.parm (not used)
+
+GAB:
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_631Gdp.parm
+TORDPAR torsion_double_631Gdp.parm
+SIDEPAR sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k
+ELEPAR electr_631Gdp.parm
+SCPPAR scp.parm
+FOURIER fourier_opt.parm.1igd_hc_iter3_3
+SCCORPAR rotcorr_AM1.parm
+
+E0G:
+
+BONDPAR bond.parm
+THETPAR thetaml.5parm
+ROTPAR scgauss.parm
+TORPAR torsion_631Gdp.parm
+TORDPAR torsion_double_631Gdp.parm
+SIDEPAR sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_gap8g-sc
+ELEPAR electr_631Gdp.parm
+SCPPAR scp.parm
+FOURIER fourier_opt.parm.1igd_hc_iter3_3
+SCCORPAR rotcorr_AM1.parm
+
+1L2Y_1LE1:
+
+BONDPAR bond_AM1.parm
+THETPAR theta_abinitio.parm
+ROTPAR rotamers_AM1_aura.10022007.parm
+TORPAR torsion_631Gdp.parm
+TORDPAR torsion_double_631Gdp.parm
+SIDEPAR scinter_${POT}.parm
+ELEPAR electr_631Gdp.parm
+SCPPAR scp.parm
+FOURIER fourier_opt.parm.1igd_hc_iter3_3
+SCCORPAR rotcorr_AM1.parm
+
+Additionally, for 1L2Y_1LE1, the following environment variables and files are required
+to generate random conformations:
+
+THETPARPDB thetaml.5parm
+ROTPARPDB scgauss.parm
+
+For CSA, the best force field is 4P. For MD, the 1L2Y_1LE1 force field is best for
+ab initio prediction but provides medium resolution (5 A for 60-residue proteins) and
+overemphasizes beta structures and has to be run with secondary-structure-prediction
+information. For prediction of the structure of mostly alpha-protein, and for running
+dynamics of large proteins, the best is the GAB force field. All these force fields
+were trained by using our procedure of hierarchical optimization [5].
+The 4P and 1L2Y_1LE1 force fields have considerable power independent of structural class.
+The ALPHA, BETA, and ALPHABETA force fields (for CSA) were used in the CASP4 exercises
+and the CASP5 force field was used in the CASP5 exercise with some success; ALPHA
+predicts reasonably the structure of alpha-helical proteins and is still not obsolete,
+while for beta and alpha+beta structure prediction
+3P or 4P should be used, because they are cheaper and more reliable than BETA and
+ALPHABETA. The early CASP3 force field is included for historical reasons only.
+
+7. INPUT FILES
+--------------
+
+7.1. Main input data file
+-------------------------
+
+Most of the data are organized as data lists, where the data can be put
+in any order, using a series of statements of the form:
+
+KEYWORD=value
+
+for simple non-logical variables
+
+or just
+
+KEYWORD
+
+to indicate that the corresponding option is turned on. For array variables
+the assignment statement is:
+
+KEYWORD=value1,value2,...
+
+However, the data lists are unnamed and that must be placed EXACTLY in the
+order indicated below. The presence of an "&" in the 80th column of a line
+indicates that the next line will belong to the same data group. The parser
+subroutines that interpret the keywords are case insensitive.
+
+Each group of data organized as a data list is indicated as "data list format"
+input.
+
+8.1.1. Title
+------------
+Any string containing up to 80 characters. The first input line is always
+interpreted as title.
+
+8.1.2. Control data (data list format; READ_CONTROL subroutine)
+---------------------------------------------------------------
+
+8.1.2.1 Keywords to chose calculation type
+------------------------------------------
+
+OUT1FILE - only the master processor prints the output file in a parallel job
+
+MINIMIZE - if present, energy minimization will be carried out.
+
+REGULAR - regularize the read in conformation (usually a crystal or
+ NMR structure) by doing a series of three constrained minimizations,
+ to keep the structure as close as possible to the starting
+ (experimental) structure. The constraints are the CA-CA distances
+ of the initial structure. The constraints are gradually diminished
+ and removed in the last minimization.
+
+SOFTREG - regularize the read in conformation (usually a crystal or NMR
+ structure) by doing a series of constrained minimizations, with
+ additional use of soft potential and secondary structure
+ freezing, to keep the structure as close as possible to the
+ starting (experimental) structure.
+
+
+CSA - if present, the run is a CSA run. At present, this is the only
+ reliable mode of doing global conformational search with this
+ package; it is NOT recommended to use MCM or THREAD for this
+ purpose.
+
+MCMA - if present, this is a Monte Carlo Minimization (MCM) run.
+
+MULTCONF- if present, conformations will be read from the INPUT.intin
+ file.
+
+MD - run canonical MD (single or multiple trajectories)
+
+RE - run REMD or MREMD (parallel jobs only)
+
+MUCA - run multicanonical MD calculations (parallel jobs only)
+
+MAP=number (integer)
+Conformational map will be calculated in chosen angles.
+
+THREAD=number (integer)
+Threading or threading-with-minimization run, using a database of structures
+contained in the $DD/patterns.cart pattern data base (502 chains or chain
+fragments), using a total number patterns. It is recommended to use this with
+energy minimization; this implies regularization of each minimized pattern.
+For references see A. Liwo, M.R. Pincus, R.J. Wawak,
+S. Rackovsky, St. Oldziej, H.A. Scheraga, J. Comput. Chem., 1997, 18, 874-887
+and A. Liwo, St. Oldziej, R. Kazmierkiewicz, M. Groth, C. Czaplewski,
+Acta Biochim. Pol., 1997, 44, 527-547.
+
+CHECKGRAD - compare numerical and analytical gradient; to be followed by:
+ CART - energy gradient in virtual-bond vectors (Cartesian coordinates)
+ INT - energy gradient in internal coordinates (default)
+ CARINT - derivatives of the internal coordinates in the virtual-bond vectors.
+
+8.1.2.2 Specification of protein and structure output in non-MD applications
+----------------------------------------------------------------------------
+
+ONE_LETTER - one-letter and not three-letter code of the amino-acid residues
+ is used
+
+SYM (1) - number of chains with same sequence (for oligomeric proteins only),
+
+PDBSTART - the initial conformation is read in from a PDB file
+
+UNRES_PDB - the starting conformation is in UNRES representation (Calpha
+ and SC coordinates only). This keyword MUST appear in such a case
+ or the program will generate erroneous and unrealistic side-chain
+ coordinates.
+
+RAND_CONF- start from a random conformation
+
+EXTCONF - start from an extended chain conformation
+
+PDBOUT - if present, conformations will be output in PDB format. Note that
+ this keyword affects only the output from single energy evaluation,
+ energy minimization and multiple-conformation data. To request
+ conformations from MD/MREMD runs in PDB format, the MDPDB keyword
+ must be placed on the MD input record.
+
+MOL2OUT - if present, conformations will be output in SYBYL mol2 format
+
+REFSTR - if present, reference structure will be read (e.g., to monitor
+ the RMS deviation from the crystal structure)
+
+PDBREF - if present, a reference structure will be read in to compare
+ the calculated conformations with it
+
+UNRES_PBD - the starting/reference structure is read from an UNRES-generated
+ PDB file
+
+Keywords: PDBOUT, MOL2OUT, PDBREF, and PDBSTART are ignored for a CSA run.
+Output mode for MD version is specified in MD input (see section 5.5).
+
+8.1.2.3. Miscellaneous
+----------------------
+
+CONSTR_DIST=number
+0 - no distance restraints
+>0 imposes harmonic restraints on selected distances; see section 5.12.
+In MD version, also restraints on the q variable [18] can be used.
+
+WEIDIS=number (real)
+the weight of the distance term; applies for REGULARIZE and THREAD, otherwise
+ignored.
+
+USE_SEC_PRED - use secondary-structure prediction information.
+
+SEED=number (integer) (no default)
+Random seed (required, even if the run is not a CSA, MCM, MD or MREMD run)
+
+PHI - only the virtual-bond dihedral angles gamma are considered as
+ variables in energy minimization
+
+BACK - only the backbone virtual angles (virtual-bond angles theta and
+ virtual-bond dihedral angles gamma) are considered as variables
+ in energy minimization
+
+By default, all internal coordinates: theta, gamma, and the side-chain
+centroid polar angles alpha and beta are considered as variables in energy
+minimization.
+
+RESCALE_MODE=number (real)
+Choice of the type of temperature dependence of the force field.
+0 - no temperature dependence
+1 - homographic dependence (not implemented yet with any force field)
+2 - hyperbolic tangent dependence [18].
+
+T_BATH=number (real)
+temperature (for MD runs and temperature-dependent force fields).
+
+The following keywords apply to MCM only:
+
+MAXGEN=number (integer) (10000)
+maximum number of conformations generated in a single MCM iteration
+
+MAXOVERLAP=number (integer) (1000)
+maximum number of conformations with "bad" overlaps allowed to appear in a
+row in a single MCM iteration.
+
+DISTCHAINMAX - (multi-chain capacity only) maximum distance between the
+ last residue of a given chain and the first residue of the
+ next chain such that restraints will not be imposed; quartic
+ restraints will be imposed for greater distances.
+
+ENERGY_DEC - detailed energies will be printed for each interacting pair
+ or each virtual bond, virtual-bond angle and dihedral angle,
+ side chain, etc. DO NOT use unless a single energy evaluation
+ was requested.
+
+8.1.3. Minimizer options (data list, subroutine READ_MINIM)
+-----------------------------------------------------------
+
+This data group is present, if MINIMIZE was specified on the control card.
+Otherwise, it must not appear.
+
+CART - minimize in virtual-bond vectors instead of angles
+
+MAXMIN=number (integer) (2000)
+maximum number of iterations of the SUMSL minimizer
+
+MAXFUN=number (integer) (5000)
+maximum number of function evaluations in a single minimization
+
+TOLF=number (real) (1.0e-2)
+Tolerance on function
+
+RTOLF=number (real) (1.0d-4)
+Relative tolerance on function
+
+The SUMSL minimizer is used in UNRES/CSA. For detailed description of
+the control parameters see the source file cored.f and sumsld.f
+
+
+8.1.4 CSA control parameters
+----------------------------
+
+This data group should be present only, if CSA was specified on the control
+card. It is recommended that the readers to read publications on CSA method
+for more complete description of the parameters. Brief description of
+parameters:
+
+NCONF=number (integer) (50)
+This corresponds to the size of the bank at the beginning of the
+CSA procedure. The size of the bank, nbank, is set to nconf.
+If necessary (at much later stages of the CSA: see icmax below),
+nbank increases by multiple of nconf.
+
+JSTART=number (integer) (1)
+JEND=number (integer) (1)
+This corresponds to the limit values of do loop, each of which
+corresponds to an separate CSA run. If jstart=1, and jstart=100,
+this routine will repeat 100 separate CSA runs (limited by CPU)
+each one with separate random number initialization.
+The only difference between two CSA runs (one with jstart=jend=1
+and another one with jstart=jend=2) would be different random
+number initializations if other parameters are identical.
+
+NSTMAX=number (integer) (500000)
+This is to set a limit the total number of local minimizations of CSA
+before termination.
+
+N1=number (integer) (6)
+N2=number (integer) (4)
+N3=number (integer) (0)
+N4=number (integer) (0)
+N5=number (integer) (0)
+N6=number (integer) (10)
+N7=number (integer) (0)
+N8=number (integer) (0)
+N9=number (integer) (0)
+IS1=number (integer) (1)
+IS2=number (integer) (8)
+These numbers are used to generate trial conformations for each seed.
+See the file, "newconf.f", for more details.
+ n1: the total number of trial conformations for each seed by substituting
+ nran number of variable angles (see subroutine newconf1ab and
+ subroutine newconf1ar)
+ n2: the total number of trial conformations for each seed by substituting
+ nran number of groups of variable angles (see subroutine newconf1bb and
+ subroutine newconf1br)
+ n3: the total number of trial conformations for each seed by substituting
+ a window of residues which forms a beta-hairpin, if there is no enough
+ beta-hairpins uses the same algorithm as n6
+ n4: the total number of trial conformations for each seed by shifting the
+ turn in beta-hairpin by +/- 1 or 2 residues, if there is no enough
+ beta-hairpins uses the same algorithm as n6
+ n5: not used
+ n6: the total number of trial conformations for each seed by substituting
+ a window of residues [is1,is2] inclusive. The size of the window is
+ determined in a random fashion (see subroutine newconf_residue for
+ generation of the trial conformations)
+ n7: the total number of trial conformations for each seed by copying a
+ remote strand pair forming nonlocal beta-sheet contact
+ n8: the total number of trial conformations for each seed by copying an
+ alpha-helical segment
+ n9: the total number of trial conformations for each seed by shifting the
+ alpha-helical segment by +/- 1 or 2 residues
+
+Typical values used for a 75-residue helical protein is
+(6 4 0 0 0 10 1 26) for (n1,n2,n3,n4,n5,n6,is1,is2), respectively.
+In this example, a total of 20 trial conformations are generated for a seed
+Usually is1=1 is used for all applications, and the value of is2 is set about
+to 1/3 of the total number of residues. n3, n4 and n7 are design to help in
+case of proteins with beta-sheets
+
+NRAN0=number (integer) (4)
+NRAN1=number (integer) (2)
+IRR=number (integer) (1)
+These numbers are used to determine if the CSA stage is very early.
+One can use (4 2 1) for these values. For more details one should look into
+the file, "newconf.f", for more details.
+
+NTOTAL=number (integer) (10000)
+CUT1=number (real) (2.0)
+CUT2=number (real) (5.0)
+Annealing schedule is set in following fashion.
+The value of D_cut is reduced geometrically from 1/cut1 of D_ave (at the
+beginning) to 1/cut2 of D_ave (after ntotal number of minimizations) where
+D_ave is the average distance between two conformations in the First_bank.
+
+ESTOP=number (real) (-3000.0)
+The CSA procedure stops if a conformations with energy lower than estop is
+obtained. If the do-loop set by jstart and jend requires more than one loop,
+the program will go on until the do-loop is finished.
+
+ICMAX=number (integer) (3)
+The maximum value of cycle (see the original publications for details).
+If the number of cycle exceeds this value the program will add nconf
+more conformations to Bank and First_bank to continue CSA procedure if
+the new size of the nbank is within the maximum set by nbankm (see above).
+If the size of nbank exceeds the maximum set by nbankm the CSA procedure
+for this run will stop and next CSA will begin depending on the do-loop
+set by jstart and jend.
+
+IRESTART=number (integer) (0)
+This tells you if the run is fresh start (irestart=0) or a restart (irestart=1)
+starting from an old results
+
+NDIFF=number (integer) (2)
+The number of variables use in comparison when structure is added to the
+bank,4 - all angels, 2 - only backbone angles gamma and theta
+
+NBANKTM=number (integer) (0)
+The maximum number of structures saved in *.CSA.bankt as history of the run
+Do not use bankt on massively parallel computation as it kills scalability.
+
+DELE=number (real) (20.0)
+Energy cutoff for bankt.
+
+DIFCUT=number (real) (720.0)
+Angle cutoff for bankt.
+
+IREF=number (integer) (0)
+0 - normal run, 1 - local CSA which generates only structures close to the
+reference one read from *.CSA.native.int file
+
+RMSCUT=number (real) (4.0)
+CA RMSD cut off used in local CSA
+
+PNCCUT=number (real) (0.5)
+Percentage of native contact used in local CSA
+
+NCONF_IN=number (integer) (0)
+The number of conformation read for the first bank from the input file
+*.intin
+
+Optionally, the CSA parameters can be read from file INPUT.CSA.in, if
+this file exists. If so, they are read in free format in the following
+order:
+
+nconf
+jstart,jend
+nstmax
+n1,n2,n3,n4,n5,n6,n7,n8,is1,is2
+nran0,nran1,irr
+nseed
+ntotal,cut1,cut2
+estop
+icmax,irestart
+ntbankm,dele,difcut
+iref,rmscut,pnccut
+ndiff
+
+
+8.1.5. MCM data (data list, subroutine MCMREAD)
+-----------------------------------------------
+
+This data group is present, if MCM was specified on the control card.
+Otherwise it must not appear.
+
+MAXACC=number (integer) (100)
+Maximum number of accepted conformations
+
+MAXTRIAL=number (integer) (100)
+Maximum number of unsuccessful trials in a row
+
+MAXTRIAL_ITER=number (integer) (1000)
+Maximum number of unsuccessful trials in a single iteration
+
+MAXREPM=number (integer) (200)
+Maximum number of repetitions of the same minimum
+
+RANFRACT=number (real) (0.5d0)
+Fraction of chain-rebuild motions
+
+OVERLAP=number (real) (1.0d3)
+Bad contact energy criterion
+
+NSTEPH=number (integer) (0)
+Number of heating step in adaptive sampling
+
+NSTEPC=number (integer) (0)
+Number of cooling step in adaptive sampling
+
+TMIN=number (real) (298.0d0)
+Minimum temperature in adaptive-temperature sampling)
+
+TMAX=number (real) (298.0d0)
+Maximum temperature in adaptive-temperature sampling)
+
+The temperature is changed according to the formula:
+
+T = TMIN*EXP(ISTEPH*(TMAX-TMIN)/NSTEPH) when heating
+
+and
+
+T = TMAX*EXP(-ISTEPC*(TMAX-TMIN)/NSTEPC) when cooling
+
+The default is to use a constant temperature.
+
+NWINDOW=number (integer) (0)
+Number of windows in which the variables will be perturbed; the windows are
+defined by the numbers of the respective amino-acid residues. If NWINDOW
+is nonzero, after specifying all MCM input the next lines must define the
+windows. Each line looks like this:
+
+winstart winend (free format)
+
+e.g. if NWINDOW=2, the input:
+
+4 10
+15 20
+
+will mean that only the variables of residues 4-10 and 15-20 will be perturbed.
+However, in general, all variables will be considered in minimization.
+
+PRINT_MC=number (0)
+Printout level in MCM. 0 - no intermediate printing, 1 and 2 - moderate
+printing, 3 - extensive printing.
+
+NO_PRINT_STAT - no output to INPUT_POTENTIALxxx.stat.
+
+NO_PRINT_INT - no internal-coordinate output to INPUT_POTENTIALxxx.int.
+
+8.1.6. MD data (subroutine READ_MDPAR)
+--------------------------------------
+
+NSTEP (1000000) number of time steps per trajectory.
+
+NTWE (100) NTWX (1000) frequency of energy and coordinate output, respectively.
+The coordinates are dumped in the pdb or compressed Gromacs (cx) format,
+depending on the next keyword.
+NTWE=0 means no energy dump.
+
+MDPDB - dump coordinates in the PDB format (cx otherwise)
+
+TRAJ1FILE only the master processor outputs coordinates. This feature pertains
+ only to REMD/MREMD jobs and overrides NTWX; coordinates are dumped at every
+ exchange in MREMD.
+
+REST1FILE only the master writes the restart file
+
+DT (real) (0.1) time step; the unit is "molecular time unit" (mtu); 1 mtu = 48.9 fs
+
+DAMAX (real) (1.0) maximum allowed change of acceleration during a single time step.
+The time step gets scaled down, if this is exceeded.
+
+DVMAX (real) (20.0) maximum allowed velocity (in A/mtu)
+
+EDRIFTMAX (real) (10.0) maximum allowed energy drift in a single MD step (10 kcal/mol)
+
+REST restart flag. The calculation is restarted if present.
+
+LARGE very detailed output. Don't use except for debugging.
+
+PRINT_COMPON prints energy components.
+
+RESET_MOMENT (1000) frequency of zeroing out the total angular momentum when
+running Berendsen mode calculations (for Langevin calculations meaningless).
+
+RESET_VEL=number (integer) (1000) - frequency of resetting velocities to values
+from Gaussian distribution.
+
+RATTLE - use RATTLE algorithm (constraint bonds); not yet implemented.
+
+RESPA - use the Multiple Time Step (MTS) or Adaptive Multiple Time Step (A-MTS)
+algorithm [17]. Without this flag the variable time step (VTS) [14] is run.
+
+NTIME_SPLIT=number (integer) (1) - initial number of time-split steps
+
+MAXTIME_SPLIT=number(integer) (64) - maximum number of time-split step
+
+If NTIME_SPLIT==MAXTIME_SPLIT, MTS is run.
+
+R_CUT=number (real) (2.0) - the cut-off distance in splitting the forces into short- and
+long-range in site-site VDW distance units.
+
+LAMBDA (real) (0.3) - the transition length (in site-site VDW distance units) between
+short- and long-range forces.
+
+XIRESP - flag to use MTS/A-MTS with Nose-Hoover/Nose-Poincare thermostats.
+
+LANG=number (integer) (0) Langevin dynamics flag:
+
+0 - No explicit Langevin dynamics.
+1 - Langevin with direct integration of the equations of motion (recommended
+ for Langevin calculations)
+2 - Langevin calculation with analytical pre-integration of the friction and
+ stochastic part of the equations of motion using an algorithm adapted from TINKER.
+ This is MUCH MORE time- and memory-consuming than 1 and requires compiling without
+ the -DLANG0 flag and enormously increases memory requirements.
+3 - The stochastic integrator developed by Cicotti and coworkers.
+4 - for other stochastic integrators (not used at present).
+
+Note: With the enclosed code, the -DLANG0 compiler flag is included which disables
+LANG=2 and LANG=3
+
+TBF Berendsen thermostat.
+
+TAU_BATH (1.0) (units are mtus; 1mtu=48.9 fs) constant of the coupling to the thermal bath
+ used with the Berendsen thermostat.
+
+NOSEPOINCARE99 - the Nose-Poincare thermostat as of 1999 will be used.
+
+NOSEPOINCARE01 - the Nose-Poincare thermostat as of 2001 will be used.
+
+NOSEHOOVER96 - the Nose-Hoover thermostat will be used.
+
+Q_NP=number (real) (0.1) - the value of the mass of the fictitious particle in the calculations
+ with the Nose-Poincare thermostat.
+
+T_BATH (300.0) (in K) temperature of canonical simulation or temperature to generate
+velocities.
+
+ETAWAT (0.8904) viscosity of water (in centipoises)
+
+RWAT (1.4) radius of water molecule (in A)
+
+SCAL_FRIC=number (real) (0.02) - scaling factor of the friction coefficients.
+
+SURFAREA - scale friction acting on atoms by atoms' solvent accessible area.
+
+RESET_FRICMAT=number (integer) (1000) - recalculate friction matrix every RESET_FRICMAT MD steps.
+
+USAMPL restraints on q (see reference 5 for meaning) will be imposed (see section .
+In this case, the next records specify the restraints; these records are
+placed before the list of temperatures or numbers of trajectories.
+
+EQ_TIME=number (real) (1.0e4) time (in mtus; 1 mtu=48.9 fs) after which restraints
+on q will start to be in force.
+
+If USAMPL has been specified, the following information must be supplied after the
+main MD input data record (subroutine READ_FRAGMENTS):
+
+Line 1: nset, npair, nfrag_back (number of sets of restraints, number of restrained
+fragments, number of restrained pairs, number of restrained backbone fragments
+(in terms of theta and gamma angles)
+
+For each set of restraints (1, 2,..., nset):
+
+mset(iset) - how many times the set is multiplied
+
+wfrag(i,iset), ifrag(1,i,iset), ifrag2(2,i,iset),qfrag(i,iset)
+weight of the restraint, first and last residue of the fragment, target q value.
+This information is repeated through nfrag.
+
+wpair(i,iset), ipair(1,i,iset), ipair(2,i,iset),qinpair(i,iset)
+weight of the restraint, first and second fragment of the pair (according to fragment
+list), target q value. This information is repeated through npair
+
+wfrag_back(1,i,iset), wfrag_back(2,i,iset), wfrag_back(3,i,iset),
+ifrag_back(1,i,iset),ifrag_back(2,i,iset)
+weight of the restraints on theta angles, weight on the restraints on gamma angles,
+weight of the restraints on side-chain rotamers, first residue of the fragment,
+last residue of the fragment. This information is repeated through nfrag_back.
+
+8.1.7 REMD/MREMD data (subroutine READ_REMDPAR)
+-----------------------------------------------
+
+NREP (3) number of replicas in a REMD/MREMD run
+
+NSTEX (1000) number of steps after which exchange is performed in REMD/MREMD
+ runs
+
+The temperatures in replicas can be specified through
+
+RETMIN (10.0) minimum temperature in a REMD/MREMD run
+
+RETMAX (1000.0) maximum temperature in a REMD/MREMD run
+
+Then the range from retmin to retmax is divided into equal segments and
+temperature of the replicas assigned accordingly,
+
+or
+
+TLIST means that the NREP temperature of the replicas will be input in the
+next record
+
+MLIST numbers of trajectories per each of the NREP temperatures will be
+specified in the record after the list of temperatures; this specifies
+a MREMD run.
+
+Important! The number of processors must be exactly equal to the number of
+trajectories, i.e., NREP for a REMD run or sum_i mlist(i) for a MREMD run.
+
+SYNC - all trajectories will be synchronized every NSTEX time steps
+(by default, they are not synchronized)
+
+TRAJ1FILE only the master processor outputs coordinates. This feature pertains
+ only to REMD/MREMD jobs and overrides NTWX; coordinates are dumped at every
+ exchange in MREMD.
+
+REST1FILE only the master writes the restart file
+
+HREMD - Hamiltonian replica exchange flag; not only temperatures but also
+sets energy-term weights are exchanged between conformations.
+
+TONLY - run a "fake" HREMD with many sets of energy-term weights in a
+single run but only temperature exchange.
+
+8.1.8 Energy-term weights (data list; subroutine MOLREAD)
+---------------------------------------------------------
+
+WLONG=number (real) (1.0d0)
+common weight of the U(SC-SC) (side-chain side-chain interaction)
+and U(SC,p) (side-chain peptide-group) term
+
+WSCC = number (real) (WLONG)
+weight of the U(SC-SC) term
+
+WSCP = number (real) (WLONG)
+weight of the U(SC-p) term
+
+WELEC=number (real) (1.0d0)
+weight of the U(p-p) (peptide-group peptide-group interaction) term
+
+WEL_LOC=number (real) (1.0d0)
+weight of the U_el_loc^3 (local-electrostatic cooperativity, third-order) term
+
+WCORRH=number (real) (1.0d0)
+weight of the U(corr) (cooperativity of hydrogen-bonding interactions, fourth-order) term
+
+WCORR5=number (real) (0.0d0)
+weight of the U_el_loc^5 (local-electrostatic cooperativity, 5th order
+contributions)
+
+WCORR6=number (real) (0.0d0)
+weight of the U_el_loc^6 (local-electrostatic cooperativity, 6th order
+contributions)
+
+WTURN3=number (real) (1.0d0)
+weight of the U_turn^3 (local-electrostatic cooperativity within 3 residue
+segment, 3rd order contribution)
+
+WTURN4=number (real) (1.0d0)
+weight of the U_turn^4 (local-electrostatic cooperativity within 4 residue
+segment, 4rd order contributions)
+
+WTURN6=number (real) (1.0d0)
+weight of the U_turn^6 (local-electrostatic cooperativity within 6 residue
+segment, 6rd order contributions)
+
+WTOR=number (real) (1.0d0)
+weight of the torsional term U(tor)
+
+WANG=number (real) (1.0d0)
+weight of the virtual-bond angle bending term U(b)
+
+WSCLOC=number (real) (1.0d0)
+weight of the side-chain rotamer term U(SC)
+
+WSTRAIN=number (real) (1.0d0)
+scaling factor of the distance-constrain or disulfide-bond strain energy term
+
+SCALSCP=number (real) (1.0d0)
+scaling factor of U(SC,p); this is an alternative to specifying WSCP; in
+this case WSCP will be calculated as WLONG*SCALSCP
+
+SCAL14=number (real) (1.0d0)
+scaling factor of the 1,4 SC-p interactions
+
+CUTOFF (7.0) - cut-off on backbone-electrostatic interactions to compute 4-
+and higher-order correlations
+
+DELT_CORR (0.5) - thickness of the distance range in which the energy is
+decreased to zero
+
+The defaults are NOT the recommended values. No "working" default values
+have been set, because the force field is still under development. The values
+corresponding to the force fields listed in section 4 are as follows:
+
+CASP3:
+WELEC=1.5 WSTRAIN=1.0 WTOR=0.08617 WANG=0.10384 WSCLOC=0.10384 WCORR=1.5 &
+WTURN3=0 WTURN4=0 WTURN6=0 WEL_LOC=0 WCORR5=0 WCORR6=0 SCAL14=0.40 SCALSCP=1.0 &
+CUTOFF=7.00000 WSCCOR=0.0
+
+ALPHA:
+WSC=1.00000 WSCP=0.72364 WELEC=1.10890 WANG=0.68702 WSCLOC=1.79888 &
+WTOR=0.30562 WCORRH=1.09616 WCORR5=0.17452 WCORR6=0.36878 WEL_LOC=0.19508 &
+WTURN3=0.00000 WTURN4=0.55588 WTURN6=0.11539 CUTOFF=7.00000 WCORR4=0.0000 &
+WTORD=0.0 WSCCOR=0.0
+
+BETA:
+WSC=1.00000 WSCP=1.10684 WELEC=0.70000 WANG=0.80775 WSCLOC=1.91939 &
+WTOR=3.36070 WCORRH=2.50000 WCORR5=0.99949 WCORR6=0.46247 WEL_LOC=2.50000 &
+WTURN3=1.80121 WTURN4=4.35377 WTURN6=0.10000 CUTOFF=7.00000 WCORR4=0.00000 &
+WSCCOR=0.0
+
+ALPHABETA:
+WSC=1.00000 WSCP=1.43178 WELEC=0.41501 WANG=0.37790 WSCLOC=0.12880 &
+WTOR=1.98784 WCORRH=2.50526 WCORR5=0.23873 WCORR6=0.76327 WEL_LOC=2.97687 &
+WTURN3=0.09261 WTURN4=0.79171 WTURN6=0.01074 CUTOFF=7.00000 WCORR4=0.00000 &
+WSCCOR=0.0
+
+CASP5:
+WSC=1.00000 WSCP=1.54864 WELEC=0.20016 WANG=1.00572 WSCLOC=0.06764 &
+WTOR=1.70537 WTORD=1.24442 WCORRH=0.91583 WCORR5=0.00607 WCORR6=0.02316 &
+WEL_LOC=1.51083 WTURN3=2.00764 WTURN4=0.05345 WTURN6=0.05282 WSCCOR=0.0 &
+CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
+
+3P:
+WSC=1.00000 WSCP=2.85111 WELEC=0.36281 WANG=3.95152 WSCLOC=0.15244 &
+WTOR=3.00008 WTORD=2.89863 WCORRH=1.91423 WCORR5=0.00000 WCORR6=0.00000 &
+WEL_LOC=1.72128 WTURN3=2.99827 WTURN4=0.59174 WTURN6=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
+
+4P:
+WSC=1.00000 WSCP=2.73684 WELEC=0.06833 WANG=4.15526 WSCLOC=0.16761 &
+WTOR=2.99546 WTORD=2.89720 WCORRH=1.98989 WCORR5=0.00000 WCORR6=0.00000 &
+WEL_LOC=1.60072 WTURN3=2.36351 WTURN4=1.34051 WTURN6=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
+
+GAB:
+WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &
+WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &
+WVDWPP=0.11371 WHPB=1.00000 &
+CUTOFF=7.00000 WCORR4=0.00000
+
+E0G:
+WLONG=1.70905 WSCP=2.18310 WELEC=1.06684 WBOND=1.00000 WANG=1.17536 &
+WSCLOC=0.22070 WTOR=2.65798 WTORD=2.00646 WCORRH=0.23541 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.42789 WTURN3=1.68126 WTURN4=0.75080 WTURN6=0.00000 &
+WVDWPP=0.27044 WHPB=1.00000 WSCP14=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000
+
+1L2Y_1LE1:
+WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &
+WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &
+WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 &
+CUTOFF=7.00000 WCORR4=0.00000
+
+8.1.9. Input and/or reference PDB file name (text format; subroutine MOLREAD)
+-----------------------------------------------------------------------------
+
+If PDBSTART or PDBREF was specified in the control card, this line contains
+the PDB file name. Trailing slashes to specify the full path are permitted.
+The file name can contain up to 64 characters.
+
+8.1.10. Amino-acid sequence (free and text format)
+--------------------------------------------------
+
+This data appears, if PDBSTART was not specified, otherwise must not be present
+because the sequence would be taken from the PDB file. The first line contains
+the number of amino-acid residues, including the end groups (free format),
+the next lines contain the sequence in 20(1X,A3) format for the three-letter
+or 80A1 format for the one-letter code. There are two types of end-groups:
+Gly (three-letter code) or G (one-letter code), if an end group contains a full
+peptide bond (e.g., the acetyl N-terminal group or the carboxyamide C-terminal
+group) and D (in the three-letter code) or X (in the one-letter code), if the
+end group does not contain a peptide group (e.g., the NH2 N-terminal end group
+or the COOH C-terminal end group). (Note the Gly or G also denotes the regular
+glycine residue, if found in the middle of a chain).
+In the second case the end group is considered as a "dummy" group and serves
+only to define the first (last) virtual-bond dihedral angle gamma for the
+first (last) full amino-acid residue.
+
+Consider, for example, the Ac-Ala(19)-NHMe polypeptide. The three-letter code
+input will look like this:
+
+21
+ Gly Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala
+ Gly
+
+And the one-letter code input will be:
+
+21
+GAAAAAAAAAAAAAAAAAAAG
+
+If the sequence is changed to NH3(+)-Ala(19)-COO(-), the inputs will look
+like this:
+
+21
+ D Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala
+ D
+
+and
+
+21
+XAAAAAAAAAAAAAAAAAAAX
+
+The sequence input is case-insensitive, because the present version of UNRES
+considers each amino-acid residue as an L-residue (there are no torsional
+parameters for the combinations of the D- and L-residues yet). Furthermore,
+each peptide group is considered as a trans group.
+
+If the version of UNRES has multi-chain capacity, placing a dummy residue
+inside the sequence indicates start of a new chain. For example, a system
+composed of two Ala(10) chains can be specified as follows (3-letter code):
+
+23
+ D Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala D Ala Ala Ala Ala Ala Ala Ala Ala
+ Ala Ala D
+
+or (1-letter code)
+
+23
+XAAAAAAAAAAXAAAAAAAAAAX
+
+
+8.1.11. Disulfide-bridge information (free format; subroutine READ_BRIDGE)
+--------------------------------------------------------------------------
+
+1st line:
+NS,(ISS(i),i=1,NS)
+
+NS - the number of half-cystines (required even if no half-cystines are present)
+
+ISS(i) - the position of ith half-cystine in the sequence (starting from the
+N-terminal end group)
+
+next line(s) (present only, if ns>0 and must not appear otherwise):
+NSS,(IHPB(i),JHPB(i),i=1,NSS)
+
+NSS - the number of disulfide bridges; must not be greater than NS/2
+
+IHPB(i),JHPB(i) - the cystine residue forming the ith bridge.
+
+The program will check, whether the residues specified in the ISS list
+are cystines and terminate with error, if any of them is not. The program
+also checks, if the numbers from the IHPB and the JHPB lists have appeared
+in the ISS list.
+
+8.1.12. Dihedral-angle restraint data (free format; subroutine MOLREAD)
+-----------------------------------------------------------------------
+
+This set of data specifies the harmonic constraints (if any) imposed on selected
+virtual-bond dihedral angles gamma.
+
+1st line:
+NDIH_CONSTR - the number of restrained gamma angles (required even if no
+restrains are applied).
+
+2nd line (present only, if NDIH_CONSTR > 0; must not appear otherwise):
+FTORS - the force constant expressed in kcal/(mol*rad**2)
+
+next NDIH_CONSTR lines (present only, if NDIH_CONSTR > 0):
+
+IDIH_CONSTR(i),PHI0(i),DRANGE(i)
+
+IDIH_CONSTR(i) - the number of ith restrained gamma angle. The angles are
+numbered after the LAST alpha-carbons. Thus, the first "real" angle has number
+4 and it corresponds to the rotation about the CA(2)-CA(3) virtual-bond axis
+and the last angle has the number NRES and corresponds to the rotation about
+the CA(NRES-2)-CA(NRES-1) virtual-bond axis.
+
+PHI0(i) - the "center" of the restraint (expressed in degrees)
+
+DRANGE(i) - the "flat well" range of the restraint (in degrees)
+
+The restraint energy for the ith restrained angle is expressed as:
+
+ /
+ | FTORS*(GAMMA(IDIH_CONSTR(i))-PHI0(i)+DRANGE(i))**2,
+ | if GAMMA(IDIH_CONSTR(i))<PHI0(i)-DRANGE(i)
+ |
+EDIH = < 0, if PHI0(i)-DRANGE(i) <= GAMMA(IDIH_CONSTR(i) <= PHI0(i)+DRANGE(i)
+ |
+ | FTORS*(GAMMA(IDIH_CONSTR(i))-PHI0(i)-DRANGE(i))**2,
+ | if GAMMA(IDIH_CONSTR(i))>PHI0(i)+DRANGE(i)
+ \
+
+Applying dihedral-angle constraints also implies that for ith constrained
+gamma angle the sampling be carried out from the
+[PHI0(i)-DRANGE(i)..PHI0(i)+DRANGE(i)] interval and not from the [-Pi..Pi]
+interval, if random conformations are generated. If only this and not
+restrained minimization is required, just set FTORS to 0.
+
+8.1.13 Distance restraints (subroutine READ_DIST_CONSTR)
+--------------------------------------------------------
+
+Restraints are imposed on Calpha...Calpha distances.
+
+NDIST=number (integer) (0) - number of restraints on specific distances.
+
+NFRAG=number (integer) (0) - number of distance-restrained protein segments.
+
+NPAIR=number (integer) (0) - number of distance-restrained pairs of segments.
+ Specifying NPAIR requires specification of segments.
+
+IFRAG=start(1),end(1),start(2),end(2)...start(NFRAG),end(NFRAG) (integers)
+First and last residues of the distance restrained segments.
+
+WFRAG=w(1),w(2),...,w(NFRAG) (reals) - force constants or bases for force
+constant calculation corresponding to fragment restraints.
+
+IPAIR=start(1),end(1),start(2),end(2),...,start(NPAIR),end(NPAIR) (integers)
+numbers of segments (consecutive numbers of start or end pairs in IFRAG
+specification), the distances between which will be restrained.
+
+WPAIR=w(1),w(2),...,w(NFRAG) (reals) - force constants or bases for force
+constant calculation corresponding to pair restraints.
+
+DIST_CUT=number (real) (5.0) - the cut-off distance in angstroms for force-
+constant calculations.
+
+The force constants within fragments/between pairs of fragments are calculated
+depending on the value of DIST_CONSTR described in section 5.1:
+
+1 - all force constants are equal to the respective entries of WFRAG/WPAIR
+
+2 - the force constants are equal to the respective entries of WFRAG/WPAIR
+ when the distance between the Calpha atoms in the reference structure
+ <=D_CUT, 0 otherwise.
+
+3 - the force constants are calculated from the formula:
+
+k(CA_j,CA_k)=W*exp{-[d(CA_j,CA_k)/DIST_CUT)]**2/2}
+
+where k(CA_j,CA_k) is the force constant between the respective Calpha atoms,
+d(CA_j,CA_k) is the distance between these Calpha atoms in the reference
+structure, and W is the basis for force-constant calculation (see above).
+
+If NDIST>0, the restraints on specific distance are subsequently input:
+
+ihpb(i), jhpb(i), forcon(i), i=1,NDIST
+
+where ihpb(i) and jhpb(i) are the numbers of the residues the distance
+between the Calpha atoms of which will be distance restrained and forcon(i)
+is the respective force constant.
+
+8.1.14 Internal coordinates of the reference structure (free format;
+--------------------------------------------------------------------
+ subroutine READ_ANGLES)
+ -----------------------
+
+This part of the data is present, if REFSTR, but not PDBREF was specified,
+otherwise must not appear. It contains the following group of variables:
+
+(THETA(i),i=3,NRES) - the virtual-bond valence angles THETA
+(PHI(i),i=4,NRES) - the virtual-bond dihedral angles GAMMA
+(ALPH(i),i=2,NRES-1)- the ALPHA polar angles of consecutive side chains
+(OMEG(i),i=2,NRES-1)- the BETA polar angles of consecutive side chains.
+
+ALPHA(i) and OMEG(i) correspond to the side chain attached to CA(i). THETA(i)
+is the CA(i-2)-CA(i-1)-CA(i) virtual-bond angle and PHI(i) is the
+CA(i-3)-CA(i-2)-CA(i-1)-CA(i) virtual-bond dihedral angle gamma.
+
+8.1.15 Internal coordinates of the initial conformation (free format;
+---------------------------------------------------------------------
+ subroutine READ_ANGLES)
+ -----------------------
+
+This part of the data is present, if RAND_CONF, MULTCONF, THREAD, or PDBSTART
+were not specified, otherwise must not appear. This input is as in section 10.
+
+8.1.15.1 File name with internal coordinates of the conformations to be processed
+---------------------------------------------------------------------------------
+ (text format; subroutine MOLREAD)
+ ---------------------------------
+
+This data is present only, if MULTCONF was specified. It contains the name of
+the file with the internal coordinates. Up to 64 characters are allowed.
+The structure of the file is that of the *.int file produced by UNRES/CSA.
+See section "The structure of the INT files" for details.
+
+8.1.16 Control data for energy map construction (data lists; subroutine MAP_READ)
+---------------------------------------------------------------------------------
+
+These data lists appear, if NMAP=n was specified, where n is the number of
+variables that will be grid-searched. One list is per one variable or a
+group of variables set equal (see below):
+
+PHI - the variable is a virtual-bond dihedral angle gamma
+THE - the variable is a virtual-bond angle theta
+ALP - the variable is a side-chain polar angle alpha
+OME - the variable is a side-chain polar angle beta
+
+RES1=number (integer)
+RES2=number (integer)
+
+The range of residues for which the values will be set; all these variables
+will be set at the same value. It is required that RES2 > RES1.
+
+FROM=angle (real)
+TO=angle (real)
+
+Lower and upper limit of scanning in grid search (in degrees)
+
+NSTEP=number (integer)
+
+Number of steps in scanning along this variable/group of variables.
+
+8.2. Input coordinate files
+---------------------------
+
+At present, geometry can be input either from the external files in the PDB
+format (with the PDBSTART option) or multiple conformations can be read
+as virtual-bond-valence and virtual-bond dihedral angles when the MULTCONF
+option is used (the latter, however, implies using standard virtual-bond
+lengths as initial values). The structure of internal-coordinate files
+is the same as that of output internal-coordinate files described in section
+9.1.1.
+
+8.3. Other input files
+----------------------
+
+CSA parameters can optionally be read in free format from file INPUT.CSA.in
+(see section 8.1.4). When a CSA run is restarted, the CSA-specific output files
+also serve as input files. INPUT is the prefix of input and output files
+as explained in section 6.
+
+Restart files for MD and REMD simulations. They are read when the keyword
+RESTART appears on the MD/REMD data group (section 8.1.6).
+
+8. OUTPUT FILES
+---------------
+
+UNRES "main" output files (INPUT.out_${POT}[processor]) are log files from
+a run. They contain the information of the molecule, force field, calculation
+type, control parameters, etc.; however, not the structures produced during
+the run or their energies except single-point energy evaluation and
+minimization-related runs. The structural information is included in
+coordinate files (*.int, *.x, *.pdb, *.mol2, *.cx) and statistics files (*.stat),
+respectively; these files are further processed by other programs (WHAM,
+CLUSTER) or can be viewed by molecular viewers (pdb or mol2 files).
+
+9.1. Coordinate files
+---------------------
+
+9.1.1. The internal coordinate (INT) file
+------------------------------------------
+
+
+This file contains the internal coordinates of the conformations produced
+by UNRES in non-MD runs. The virtual-bond lengths are assumed constant so
+only the angular variables are provided (see ref
+
+IT,ENER,NSS,(IHPB(I),JHPB(I),I=1,NSS)
+(I5,F12.5,I2,9(1X,2I3))
+
+IT - the number of the conformation
+ENER - total energy
+NSS - the number of disulfide bridges
+(IHPB(I),JHPB(I),I=1,NSS) - the positions of the pairs of half-cystines
+forming the bridges. If NSS>9, the remaining pairs are written in the
+following lines in the (3X,11(1X,2I3)) format.
+
+(THETA(I),I=3,NRES)
+(8F10.4)
+
+The virtual-bond angles THETA (in degrees)
+
+(PHI(I),I=4,NRES)
+(8F10.4)
+
+The virtual-bond dihedral angles GAMMA (in degrees)
+
+(ALPH(I),I=2,NRES-1)
+(OMEG(I),I=2,NRES-1)
+(8F10.4)
+
+The polar angles ALPHA and BETA of the side-chain centers (in degrees).
+
+9.1.2. The plain Cartesian coordinate (X) files (subroutine CARTOUT)
+--------------------------------------------------------------------
+
+This file contains the Cartesian coordinates of the alpha-carbon and
+side-chain-center coordinates. All conformations from an MD/MREMD
+trajectory are collated to a single file. The structure of each
+conformation's record is as follows:
+
+1st line: time,potE,uconst,t_bath,nss,(ihpb(j),jhpb(j),j=1,nss),
+nrestr,(qfrag(i),i=1,nfrag),(qpair(i),i=1,npair),
+(utheta(i),ugamma(i),uscdiff(i),i=1,nfrag_back)
+
+time: MD time (in "molecular time units"; 1 mtu = 4.89 fs),
+potE: potential energy,
+uconst: restraint energy corresponding to restraints on Q and backbone geometry,
+(see section ??),
+t_bath: thermostat temperature,
+nss: number of disulfide bonds,
+ihpb(j), jhpb(j): the numbers of linked cystines for jth disulfide bond,
+nrestr: number of restraints on q and local geometry,
+qfrag(i): q value for ith fragment,
+qpair(i): q value for ith pair,
+utheta(i): sum of squares of the differences between the theta angles
+ of the current conformation from those of the experimental conformation,
+ugamma(i): sum of squares of the differences beaten the gamma angles
+ of the current conformation from those of the experimental conformation,
+uscdiff(i): sum of squares of the differences between the Cartesian difference
+ of the unit vector of the Calpha-SC axis of the current conformation from
+ those of the experimental conformation.
+
+Next lines: Cartesian coordinates of the Calpha atoms (including dummy atoms)
+(sequentially, 10 coordinates per line)
+Next lines: Cartesian coordinates of the SC atoms (including glycines and
+dummy atoms) (sequentially, 10 coordinates per line)
+
+9.1.3. The compressed Cartesian coordinate (CX) files
+-----------------------------------------------------
+
+These files are compressed binary files (extension cx). For each conformation,
+the items are written in the same order as specified in section 9.1.2. For
+MREMD runs, if TRAJ1FILE is specified on MREMD record (see section 8.1.6),
+snapshots from all trajectories are written every time the coordinates
+are dumped. Thus, the file contains snapshot 1 from trajectory 1, ...,
+snapshot 1 from trajectory M, snapshot 2 from trajectory 1, ..., etc.
+
+The compressed cx files can be converted to pdb file by using the xdrf2pdb
+auxiliary program (single trajectory files) or xdrf2pdb-m program (multiple
+trajectory files from MREMD runs generated by using the TRAJ1FILE option).
+The multiple-trajectory cx files are also input files for the auxiliary
+WHAM program.
+
+9.1.4. The Brookhaven Protein Data Bank format (PDB) files (subroutine PDBOUT)
+------------------------------------------------------------------------------
+
+These files are written in PDB standard (see. e.g.,
+ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf).
+The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used.
+The Calpha (marked CA) and SC (marked CB) coordinates are output. The CONECT
+records specify the Calpha...Calpha and Calpha...SC virtual bonds. Secondary
+structure is detected based on peptide-group contacts, as specified in
+ref 12. Dummy residues are omitted from the output. If the program has
+multiple-chain function, the presence of a dummy residue in a sequence
+starts a new chain, which is assigned the next alphabet letter as ID, and
+residue numbering is started over.
+
+9.1.5. The SYBYLL (MOL2) files
+------------------------------
+
+See the description of mol2 format (e.g.,
+http://tripos.com/data/support/mol2.pdf). Similar remarks apply as for
+the PDB format (section 9.1.4).
+
+9.2. The summary (STAT) file
+----------------------------
+
+9.2.1. Non-MD runs
+------------------
+
+This file contains a short summary of the quantities characterizing the
+conformations produced by UNRES/CSA. It is created for MULTCONF and MCM.
+
+NOUT,EVDW,EVDW2,EVDW1+EES,ECORR,EBE,ESCLOC,ETORS,ETOT,RMS,FRAC
+(I5,9(1PE14.5))
+
+NOUT - the number of the conformations
+
+EVDW,EVDW2,EVDW1+EES,ECORR,EBE,ESCLOC,ETORS - energy components
+
+ETOT - total energy
+
+RMS - RMS deviation from the reference structure (if REFSTR was specified)
+
+FRAC - fraction of side chain - side chain contacts of the reference
+ structure present in this conformation (if REFSTR was specified)
+
+9.2.2. MD and MREMD runs
+-------------------------
+
+Each line of the stat file generated by MD/MREMD runs contains the following
+items in sequence:
+
+step - the number of the MD step
+
+time - time [unit is MTU (molecular time unit) equal to 48.9 fs]
+
+Ekin - kinetic energy [kcal/mol]
+
+Epot - potential energy [kcal/mol]
+
+Etot - total energy (Ekin+Epot)
+
+H-H0 - the difference between the cureent and initial extended Hamiltionian
+ in Nose-Hoover or Nose-Poincare runs; not present for other thermostats.
+
+RMSD - root mean square deviation from the reference structure (only in
+ REFSTR has been specified)
+
+damax - maximum change of acceleration between two MD steps
+
+fracn - fraction of native side-chain concacts (very crude, based on
+ SC-SC distance only)
+
+fracnn - fraction of non-native side-chain contacts
+
+co - contact order
+
+temp - actual temperature [K]
+
+T0 - initial (microcanonical runs) or thermostat (other run types)
+ temperature [K]
+
+Rgyr - radius of gyration based on Calpha coordinates [A]
+
+proc - in MREMD runs the number of the processor (the number of the
+ trajectory less 1); not present for other runs.
+
+For an USAMPL run, the following items follow the above list:
+
+iset - the number of the restraint set
+
+uconst - restraint energy pertaining to q-values
+
+uconst_back - restraint energy pertaining to virtual-backbone restraints
+
+(qfrag(i),i=1,nfrag) - q values of the specified fragments
+
+(qpair(ii2),ii2=1,npair) - q values of the specified pairs of fragments
+
+(utheta(i),ugamma(i),uscdiff(i),i=1,nfrag_back) - virtual-backbone and
+ side-chain-rotamer restraint energies of the fragments specified
+
+If PRINT_COMPON has been specified, the energy components are printed
+after the items described above.
+
+9.3. CSA-specific output files
+------------------------------
+
+There are several output files from the CSA routine:
+INPUT.CSA.seed, INPUT.CSA.history, INPUT.CSA.bank, INPUT.CSA.bank1,
+INPUT.CSA.rbank INPUT.CSA.alpha, INPUT.CSA.alpha1.
+
+The most informative outfile is INPUT.CSA.history. This file first write down
+the parameters in INPUT.CSA.csa file. Later it shows the energies of random
+minimized conformations in it's generation. After sorting the First_bank
+in energy (ascending order), the energies of the First_bank is re-written here.
+After this the output looks like:
+ 1 0 100 6048.2 1 100-224.124-114.346 202607 100 100
+ 1 0 700 5882.6 2 29-235.019-203.556 1130308 100 100
+ 1 0 1300 5721.5 2 18-242.245-212.138 2028008 100 100
+ 1 0 1900 5564.8 13 54-245.185-218.087 2897988 98 100
+ 1 0 2500 5412.4 13 61-246.214-222.068 3706478 97 100
+ 1 0 3100 5264.2 13 89-248.715-224.939 4514196 96 100
+
+Each line is written between each iteration (just after selection
+of seed conformations) containing following data:
+jlee,icycle,nstep,cutdif,ibmin,ibmax,ebmin,ebmax,nft,iuse,nbank
+ibmin and ibmax lists the index of bank conformations corresponding to the
+lowest and highest energies with ebmin and ebmax.
+nft is the total number of function evaluations so far.
+iuse is the total number of conformations which have not been used as seeds
+prior to calling subroutine select_is which select seeds.
+
+Therefore, in the example shown above, one notes that so far 3100
+minimizations has been performed corresponding to the total of 4514196
+function evaluations. The lowest and highest energy in the Bank is
+-248.715 (#13) and -224.939 (#89), respectively. The number of conformations
+already used as seeds (not including those selected as seeds in this iteration)
+so far is 4 (100-96).
+
+The files INPUT.CSA.bank and INPUT.CSA.rbank contains data of Bank and
+First_bank. For more information on these look subroutines write_bank
+and write_rbank. The file INPUT.CSA.bank is overwritten between each
+iteration whereas Bank is accumulated in INPUT.CSA.bank1 (not for every
+iteration but as specified in the subroutine together.f).
+
+The file INPUT.CSA.seed lists the index of the seed conformations with their
+energies. Files INPUT.CSA.alpha, INPUT.CSA.alpha1 are written only once
+at the beginning of the CSA run. These files contain some arrays used
+in CSA procedure.
+
+10. TECHNICAL SUPPORT CONTACT INFORMATION
+-----------------------------------------
+
+ Dr. Adam Liwo
+ Faculty of Chemistry, University of Gdansk
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.
+ phone: +48 58 523 5430
+ fax: +48 58 523 5472
+ e-mail: adam@chem.univ.gda.pl
+
+ Dr. Cezary Czaplewski
+ Faculty of Chemistry, University of Gdansk
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.
+ phone: +48 58 523 5430
+ fax: +48 58 523 5472
+ e-mail: czarek@chem.univ.gda.pl
+
+ Dr. Stanislaw Oldziej
+ Intercollegiate Faculty of Biotechnology
+ University of Gdansk, Medical University of Gdansk
+ ul. Kladki 22, 80-922 Gdansk, Poland
+ phone: +48 58 523 5361
+ fax: +48 58 523 5472
+ e-mail: stan@biotech.ug.gda.pl
+
+ Dr. Jooyoung Lee
+ Korea Institute for Advanced Study
+ 207-43 Cheongnyangni 2-dong, Dongdaemun-gu,
+ Seoul 130-722, Korea
+ phone: +82-2-958-3890
+ fax: +82-2-958-3731
+ email: jlee@kias.re.kr
+
+Prepared by Adam Liwo and Jooyoung Lee, 7/17/99
+Revised by Cezary Czaplewski 1/4/01
+Revised by Cezary Czaplewski and Adam Liwo 8/26/03
+Revised by Cezary Czaplewski and Adam Liwo 11/26/11
+Revised by Adam Liwo 02/19/12
+
--- /dev/null
+ WHAM (Weighted Histogram Analysis Method)
+ Processing results of UNRES/MREMD simulations
+ ---------------------------------------------
+
+TABLE OF CONTENTS
+-----------------
+
+1. License terms
+
+2. References
+
+3. Functions of the program
+
+4. Installation
+
+5. Running the program
+
+6. Input and output files
+ 6.1. Summary of files
+ 6.2. The main input file
+ 6.2.1. General data
+ 6.2.2 Molecule and energy parameter data
+ 6.2.2.1. General information
+ 6.2.2.2. Sequence information
+ 6.2.2.3. Dihedral angle restraint information
+ 6.2.2.4. Disulfide-bridge data
+ 6.2.3. Energy-term weights and parameter files
+ 6.2.4. (M)REMD/Hamiltonian (M)REMD setting specification
+ 6.2.5. Information of files from which to read conformations
+ 6.2.6. Information of reference structure and comparing scheme
+ 6.3. The structure of the main output file (out)
+ 6.4. The thermodynamic quantity and ensemble average (stat) files
+ 6.5. The conformation summary with classification (stat) files
+ 6.6. The histogram files
+ 6.7. The rmsd-radius of gyration potential of mean force files
+ 6.8. The PDB files
+ 6.8. The compresses Cartesian coordinates (cx) file.
+
+7. Support
+
+1. LICENSE TERMS
+----------------
+
+* This software is provided free of charge to academic users, subject to the
+ condition that no part of it be sold or used otherwise for commercial
+ purposes, including, but not limited to its incorporation into commercial
+ software packages, without written consent from the authors. For permission
+ contact Prof. H. A. Scheraga, Cornell University.
+
+* This software package is provided on an "as is" basis. We in no way warrant
+ either this software or results it may produce.
+
+* Reports or publications using this software package must contain an
+ acknowledgment to the authors and the NIH Resource in the form commonly
+used
+ in academic research.
+
+2. REFERENCES
+-------------
+
+[1] S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, J.M. Rosenberg.
+ The weighted histogram analysis method for free-energy calculations
+ on biomolecules. I. The method.
+ J. Comput. Chem., 1992, 13, 1011-1021.
+
+[2] A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, K. Wachucik,
+ H.A. Scheraga.
+ Modification and optimization of the united-residue (UNRES) potential
+ energy function for canonical simulations. I. Temperature dependence of the
+ effective energy function and tests of the optimization method with single
+ training proteins.
+ J. Phys. Chem. B, 2007, 111, 260-285.
+
+[3] S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 2. Off-lattice tests of the method with single
+ proteins. J. Phys. Chem. B., 2004, 108, 16934-16949.
+
+[4] S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 2. Off-lattice tests of the method with single
+ proteins. J. Phys. Chem. B., 2004, 108, 16934-16949.
+
+3. FUNCTIONS OF THE PROGRAM
+---------------------------
+
+The program processes the results of replica exchange (REMD) or multiplexed
+replica exchange molecular dynamics (MREMD) simulations with UNRES to compute
+the probabilities of the obtained conformations to occur at particular
+temperatures. The program is based on the variant of the weighted histogram
+analysis (WHAM) method [1] described in ref [2].
+
+The program outputs the following information:
+
+a) Temperature profiles of thermodynamic and structural ensemble-averaged
+ quantities.
+
+b) Histograms of native-likeness measure q (defined by eqs 8-11 of ref [2]).
+
+c) Optionally the most probable conformations at REMD temperatures.
+
+d) Optionally the coordinates with information to compute probabilities
+ for the conformations to occur at any temperature.
+
+The program takes usually UNRES compressed coordinate files (cx files) from
+MREMD obtained by using the TRAJ1FILE option. The user can request to
+partition the whole run into equal slices (or windows), each starting from,
+say, snapshot n (for each trajectory) and ending at snapshot n+1.
+Alternatively, the UNRES Cartesian coordinate (x files) can be input; however,
+they must contain only the analyzed portion of the trajectories; they
+are usually prepared from single trajectories by using xdrf2x.
+
+Two versions of the program are provided:
+
+a) Canonical version which treats single polypeptide chains; the source code
+is in WHAM/src directory.
+
+b) Version for oligomeric proteins; multiple chains are handled by inserting
+dummy residues in the sequence; the source code is in WHAM/src-M directory.
+
+4. INSTALLATION
+---------------
+
+Customize Makefile to your system. See section 7 of the description of UNRES
+for compiler flags that are used to created executables for a particular
+force field. There are already several Makefiles prepared for various systems
+and force fields.
+
+Run make in the WHAM/src directory WHAM/src-M directory for multichain
+version. Make sure that MPI is installed on your system; the present program
+runs only in parallel mode.
+
+5. RUNNING THE PROGRAM
+----------------------
+
+The program requires a parallel system to run. Depending on system,
+either the wham.csh C-shell script (in WHAM/bin directory) can be started
+using mpirun or the binary in the C-shell script must be executed through
+mpirun. See the wham.csh C-shell script and section 6 for the files
+processed by the program.
+
+6. INPUT AND OUTPUT FILES
+-------------------------
+
+6.1. SUMMARY OF THE FILES
+-------------------------
+
+The C-shell script wham.csh is used to run the program (see the WHAM/bin
+directory). The data files that the script needs are mostly the same as
+for UNRES (see section 6 of UNRES description). In addition, the environmental
+variable CONTFUN specifies the method to assess whether two side chains
+are at contact; if CONTFUN=GB, the criterion defined by eq 8 of ref 4 is
+used to assess whether two side chains are at contact. Also, the parameter
+files from the C-shell scripts are overridden if the data from Hamiltonian
+MREMD are processed; if so, the parameter files are defined in the main
+input file.
+
+The main input file must have inp extension. If it is INPUT.inp, the output
+files are as follows:
+
+INPUT.out_POTxxx - output files from different processors (INPUT.out_000 is the
+ main output file). POT is the identifier of the sidechain-sidechain
+ potential.
+
+INPUT_POT_GB_xxx.stat or INPUT_POT_slice_YYXXX.stat- the summary conformation-
+ classification file from processor xxx (each processor handles part of
+ conformations); the second occurs if the run is partitioned into slices.
+
+INPUT.thermal or INPUT_slice_yy.thermal - thermodynamic functions and
+ temperature profiles of the ensemble averages (the second form if the
+ run is partitioned into slices).
+
+INPUT_T_xxx.pdb or INPUT_slice_yy_T_xxx.pdb - top conformations the number
+ of these conformations is selected by the user) in PDB format.
+
+INPUT.cx - the compressed UNRES coordinate file with information to compute
+ the probability of a given conformation at any temperature.
+
+INPUT.hist INPUT_slice_xx.hist INPUT_par_yy.hist INPUT_par_yy_slice_zz.x
+ - histograms of q at MREMD temperatures.
+
+INPUT.ent INPUT_slice_xx.ent INPUT_par_yy.ent INPUT_par_yy_slice_xx.ent
+ - the histogram(s) of energy density.
+
+INPUT.rmsrgy INPUT_par_yy.rmsrgy INPUT_slice_xx.rmsrgy or
+ INPUT_par_yy_slice_xx.rmsrgy
+ - the 2D histogram(s) of rmsd from the experimental structure and radius
+ of gyration.
+
+6.2. MAIN INPUT FILE
+--------------------
+
+This file has the same structure as the UNRES input file; most of the data are
+input in a keyword-based form (see section 7.1 of UNRES description). The data
+are grouped into records, referred to as lines. Each record, except for the
+records that are input in non-keyword based form, can be continued by placing
+an ampersand (&) in column 80. Such a format is referred to as the data list
+format.
+
+In the following description, the default values are given in parentheses.
+
+6.2.1. General data (data list format)
+--------------------------------------
+
+N_ENE (N_ENE_MAX) - the number of energy components
+
+SYM (1) - number of chains with same sequence (for oligomeric proteins only),
+
+HAMIL_REP - if present, Hamiltonian process the results of replica exchange runs
+ (replicas with different parameters of the energy function)
+
+NPARMSET (1) - number of energy parameter sets (>1 only for Hamiltonian
+ replica exchange simulations)
+
+SEPARATE_PARSET - if present, HREMD was run in a mode such that only temperature
+ but not energy-function parameters was exchanged
+
+IPARMPRINT (1) - number of parameter set with which to construct conformational
+ ensembles; important only when HREMD runs are processed
+
+ENE_ONLY - if present, only conformational energies will be calculated and
+ printed; no WHAM iteration
+
+EINICHECK (2) - > 0 compare the conformational energies against those stored in
+ the coordinate file(s); 1: compare but print only a warning message if
+ different; 2: compare and terminate the program if different; 0: don't
+ compare.
+
+MAXIT (5000) - maximum number of iterations in solving WHAM equations
+
+ISAMPL (1) - input conformation sampling frequency (e.g., if ISAMPL=5, only
+ each 5th conformation will be read)
+
+NSLICE (1) - number of "slices" or "windows" into which each trajectory will
+ be partitioned; each slice will be analyzed independently
+
+FIMIN (0.001) - maximum average difference between window free energies
+ between the current and the previous iteration
+
+ENSEMBLES (0) - number of conformations (ranked according to probabilities) to
+ be output to PDB file at each MREMD temperature; 0 means that no
+ conformations will be output. Non-zero values should not be used when NSLICE>1
+
+CLASSIFY - if present, each conformation will be assigned a class, according
+to the scheme described in ref [3]
+
+DELTA (0.01) - one dimension bin size of the histogram in q
+
+DELTRMS (0.05) - rms dimension bin size in rms-radius of gyration histograms
+
+DELTRGY (0.05) - radius of gyration bin size in rms-radius of gyration histograms
+
+NQ (1) - number of q's (can be for entire molecule, fragments, and pairs of
+ fragments)
+
+CXFILE - produce the compressed coordinate file with information necessary to
+ compute the probabilities of conformations at any temperature
+
+HISTOUT - if present, the histograms of q at MREMD temperatures are
+ constructed and printed to main output file
+
+HISTFILE - if present, the histograms are also printed to separate files
+
+ENTFILE - if present, histogram of density of states (entropy) is constructed
+ and printed
+
+RMSRGYMAP - if present, 2D histograms of radius of rmsd and radius of gyration at MREMD
+ temperatures are constructed and printed
+
+WITH_DIHED_CONSTR - if present, dihedral-angle restraints were imposed in the
+ processed MREMD simulations
+
+RESCALE (1) - Choice of the type of temperature dependence of the force field.
+0 - no temperature dependence
+1 - homographic dependence (not implemented yet with any force field)
+2 - hyperbolic tangent dependence [18].
+
+6.2.2 Molecule and energy parameter data
+----------------------------------------
+
+6.2.2.1. General information
+----------------------------
+
+SCAL14 (0.4) - scale factor of backbone-electrostatic 1,4-interactions
+
+SCALSCP (1.0) - scale factor of SC-p interactions
+
+CUTOFF (7.0) - cut-off on backbone-electrostatic interactions to compute 4-
+ and higher-order correlations
+
+DELT_CORR (0.5) - thickness of the distance range in which the energy is
+decreased to zero
+
+ONE_LETTER - if present, the sequence is to be read in 1-letter code,
+ otherwise 3-letter code
+
+6.2.2.2. Sequence information
+-----------------------------
+
+1st record (keyword-based input):
+
+NRES - number of residues, including the UNRES dummy terminal residues, if present
+
+Next records: amino-acid sequence
+
+3-letter code: Sequence is input in format 20(1X,A3)
+
+1-letter code: Sequence is input in format 80A1
+
+6.2.2.3. Dihedral angle restraint information
+---------------------------------------------
+
+This is the information about dihedral-angle restraints, if any are present.
+It is specified only when WITH_DIHED_CONSTR is present in the first record.
+
+1st line: ndih_constr - number of restraints (free format)
+
+2nd line: ftors - force constant (free format)
+
+Each of the following ndih_constr lines:
+
+idih_constr(i),phi0(i),drange(i) (free format)
+
+idih_constr(i) - the number of the dihedral angle gamma corresponding to the
+ith restraint
+
+phi0(i) - center of dihedral-angle restraint
+
+drange(i) - range of flat well (no restraints for phi0(i) +/- drange(i))
+
+6.2.2.4. Disulfide-bridge data
+------------------------------
+
+1st line: NS, (ISS(I),I=1,NS) (free format)
+
+NS - number of cystine residues forming disulfide bridges
+
+ISS(I) - the number of the Ith disulfide-bonding cystine in the sequence
+
+2nd line: NSS, (IHPB(I),JHPB(I),I=1,NSS) (free format)
+
+NSS - number of disulfide bridges
+
+IHPB(I),JHPB(I) - the first and the second residue of ith disulfide link
+
+Because the input is in free format, each line can be split
+
+6.2.3. Energy-term weights and parameter files
+----------------------------------------------
+
+There are NPARMSET records specified below.
+
+All items described in this section are input in keyword-based mode.
+
+1st record: Weights for the following energy terms:
+
+WSC (1.0) - side-chain-side-chain interaction energy
+
+WSCP (1.0) - side chain-peptide group interaction energy
+
+WELEC (1.0) - peptide-group-peptide group interaction energy
+
+WEL_LOC (1.0)- third-order backbone-local correlation energy
+
+WCORR (1.0) - fourth-order backbone-local correlation energy
+
+WCORR5 (1.0) - fifth-order backbone-local correlation energy
+
+WCORR6 (1.0) - sixth-order backbone-local correlation energy
+
+WTURN3 (1.0) - third-order backbone-local correlation energy of pairs of
+ peptide groups separated by a single peptide group
+
+WTURN4 (1.0) - fourth-order backbone-local correlation energy of pairs of
+ peptide groups separated by two peptide groups
+
+WTURN6 (1.0) - sixth-order backbone-local correlation energy for pairs of
+ peptide groups separated by four peptide groups
+
+WBOND (1.0) - virtual-bond-stretching energy
+
+WANG (1.0) - virtual-bond-angle-bending energy
+
+WTOR (1.0) - virtual-bond-torsional energy
+
+WTORD (1.0) - virtual-bond-double-torsional energy
+
+WSCCOR (1.0) - sequence-specific virtual-bond-torsional energy
+
+WDIHC (0.0) - dihedral-angle-restraint energy
+
+WHPB (1.0) - distance-restraint energy
+
+2nd record: Parameter files. If filename is not specified that corresponds to
+particular parameters, the respective name from the C-shell script will be
+assigned. If no files are to be specified, an empty line must be inserted.
+
+BONDPAR - bond-stretching parameters
+
+THETPAR - backbone virtual-bond-angle-bending parameters
+
+ROTPAR - side-chain-rotamer parameters
+
+TORPAR - backbone-torsional parameters
+
+TORDPAR - backbone-double-torsional parameters
+
+FOURIER - backbone-local - backbone-electrostatic correlation parameters
+
+SCCORAR - sequence-specific backbone-torsional parameters (not used at
+ present)
+
+SIDEPAR - side-chain-side-chain-interaction parameters
+
+ELEPAR - backbone-electrostatic-interaction parameters
+
+SCPPAR - backbone-side-chain-interaction parameters
+
+6.2.4. (M)REMD/Hamiltonian (M)REMD setting specification
+--------------------------------------------------------
+
+If HAMIL_REP is present in general data, read the following group of records
+only once; otherwise, read for each parameter set (NPARSET times total)
+
+NT (1) - number of temperatures
+
+REPLICA - if present, replicas in temperatures were specified with this parameter set
+
+UMBRELLA - if present, umbrella-sampling was run with this parameter set
+
+READ_ISET - if present, umbrella-sampling-window number is read from the compressed Cartesian
+ coordinate (cx) file even if the data are not from umbrella-sampling run(s).
+ ISET is present in the cx files from the present version of UNRES.
+
+Following NT records are for consecutive temperature replicas; each record is
+organized as keyword-based input:
+
+TEMP (298.0) - initial temperature of this replica (replicas in MREMD)
+
+FI (0.0) - initial values of the dimensionless free energies for all q-restraint
+ windows for this replica (NR values)
+
+KH (100.0) - force constants of q restraints (NR values)
+
+Q0 (0.0d0) - q-restraint centers (NR values)
+
+6.2.5. Information of files from which to read conformations
+------------------------------------------------------------
+
+If HAMIL_REP is present in general data, read the following two records
+only once; otherwise, read for each parameter set (NPARSET times total)
+
+1st record (keyword-based input):
+
+For temperature replica only ONE record is read; for non-(M)REMD runs, NT
+records must be supplied. The records are in keyword-based format.
+
+NFILE_ASC - number of files in ASCII format (UNRES Cartesian coordinate (x)
+ files) for current parameter set
+
+NFILE_CX - number of compressed coordinate files (cx files) for current
+ parameter set.
+
+NFILE_BIN - number of binary coordinate files (now obsolete because it
+ requires initial conversion of ASCII format trajectories into binary format)
+
+It is strongly recommended to use cx files from (M)REMD runs with TRAJ1FILE
+option. Multitude of trajectory files which are opened and closed by different
+processors might impair file system accessibility. Should you wish to process
+trajectories each one of which is stored in a separate file, better collate
+the required slices of them first to an x file by using the xdrf2x program
+piped to the UNIX cat command.
+
+2nd record:
+
+coordinate file name(s) without extension
+
+6.2.6. Information of reference structure and comparing scheme
+-----------------------------------------------------------------
+
+The following records pertain to setting up the classification of conformation
+aimed ultimately at obtaining a class numbers. Fragments and pairs of
+fragments are specified and compared against those of reference structure in
+terms of secondary structure, number of contacts, rmsd, virtual-bond-valence
+and dihedral angles, etc. Then the class number is constructed as described in
+ref 3. A brief description of comparison procedure is as follows:
+
+1. Elementary fragments usually corresponding to elements of secondary
+or supersecondary structure are selected. Based on division into fragments,
+levels of structural hierarchy are defined.
+
+2. At level 1, each fragment is checked for agreement with the corresponding
+fragment in the native structure. Comparison is carried out at two levels:
+the secondary structure agreement and the contact-pattern agreement level.
+
+At the secondary structure level the secondary structure (helix, strand
+or undefined) in the fragment is compared with that in the native fragment
+in a residue-wise manner. Score 0 is assigned if the structure is different
+in more than 1/3 of the fragment, 1 is assigned otherwise.
+
+The contact-pattern agreement level compares the contacts between the peptide
+groups of the backbone of the fragment and the native fragment and also
+compares their virtual-bond dihedral angles gamma. It is allowed to shift
+the sequence by up to 3 residues to obtain contact pattern match. A score
+of 0 is assigned if more than 1/3 of native contacts do not occur or
+there is more than 60 deg (usually, but this cutoff can be changed) maximum
+difference in gamma. Otherwise score 1 is assigned.
+
+The total score of a fragment is an octal number consisting of bits
+hereafter referred to S (secondary structure) C (contact match) and H
+(sHift) (they are in the order HCS). Their values are as follows:
+
+S - 1 native secondary structure; 0 otherwise;
+C - 1 native contact pattern; 0 otherwise;
+H - 1 contact match obtained without sequence shift 0 otherwise.
+
+For example, octal 7 (111) corresponds to native secondary structure, native
+contact pattern, and no need to shift the sequence for contact match;
+octal 1 (001) corresponds to native secondary structure only (i.e., nonnative
+contact pattern).
+
+3. At level 2, contacts between (i) the peptide groups or (ii) the side chains
+within pairs of fragments are compared. Case (i) holds when we seek contacts
+between the strands of a larger beta-sheet formed by two fragments, case (ii)
+when we seek the interhelix or helix-beta sheet contacts. Additionally,
+the pairs of fragments are compared with their native counterparts by rmsd.
+Score 0 is assigned to a pair of fragments, if it has less than 2/3 native
+contacts and too large rmsd (a cut-off of 0.1 A/residue is set), score 1 if
+it has enough native contacts and sufficiently low rmsd, but the sequence
+has to be shifted to obtain a match, and score 2, if sufficient match is
+obtained without shift.
+
+4. At level 3 and higher, triads, quadruplets,..., etc. of fragments are
+compared in terms of rmsd from their native counterparts (the last level
+corresponds to comparing whole molecules). The score (0, 1, or 2) is assigned
+to each composite fragment as in the case of level 2.
+
+5. The TOTAL class number of a structure is a binary number composed of
+parts of scores of fragments, fragment pairs, etc. It is illustrated
+on the following example; it is assumed that the molecule has three fragment
+as in the case of 1igd.
+
+level 1 level 2 level 3
+123 123 123||1-2 1-3 2-3 1-2 1-3 2-3 || 1-2-3 | 1-2-3 ||
+sss|ccc|hhh|| c c c | h h h || r | h ||
+
+Bits s, c, and h of level 1 are explained in point 2; bits c and h of level
+2 pertain to contact-pattern match and shift; bits r and h of level 3 pertain
+to rmsd match and shift for level 3.
+
+The input is specified as follows:
+
+
+Program to classify structures
+
+1st record (keyword-based input):
+
+VERBOSE : if present, detailed output in classification (use if you want to
+ fill up the disk)
+
+PDBREF : if present, the reference structure is read from the pdb
+
+BINARY : if present, the class will be output in octal/quaternary/binary format
+ for levels 1, 2, and 3, respectively
+
+DONT_MERGE_HELICES : if present, the pieces of helices that contain only
+ small breaks of hydrogen-bonding contacts (e.g., a kink) are not merged
+ in a larger helix
+
+NLEVEL=n : number of classification levels
+
+n>0 - the fragments for n levels will be defined manually
+n<0 - the number of levels is -n and the fragments will be detected automatically
+
+START=n : the number of conformation at which to start
+
+END=n : the number of conformation at which to end
+
+FREQ=n (1) : sampling frequency of conformations; e.g. FREQ=2 means that every
+ second conformation will be considered
+
+CUTOFF_UP=x : upper boundary of rmsd cutoff (the value is per 50 residues)
+
+CUTOFF_LOW=x : lower boundary of rmsd cutoff (per 50 residues)
+
+RMSUP_LIM=x : lower absolute boundary of rmsd cutoff (regardless of fragment
+ length)
+
+RMSUPUP_LIM=x : upper absolute boundary of rmsd cutoff (regardless of fragment
+ length)
+
+FRAC_SEC=x (0.66666) the fraction of native secondary structure
+ to consider a fragment native in secondary structure
+
+2nd record:
+
+For nlevel < 0 (automatic fragment assignment):
+
+SPLIT_BET=n (0) : if 1, the hairpins are split into strands and strands are
+ considered elementary fragments
+
+ANGCUT_HEL=x (50): cutoff on gamma angle differences from the native for a helical
+ fragment
+
+MAXANG_HEL=x (60) : as above but maximum cutoff
+
+ANGCUT_BET=x (90), MAXANG_BET=x (360), ANGCUT_STRAND=xi (90), MAXANG_STRAND=x (360)
+ same but for a hairpin or sheet fragment.
+
+FRAC_MIN=x (0.6666) : minimum fraction of native secondary structure
+
+NC_FRAC_HEL=x (0.5) : fraction of native contacts for a helical fragment
+
+NC_REQ_HEL=x (0) : minimum required number of contacts
+
+NC_FRAC_BET=x (0.5), NC_REQ_BET=x (0) : same for beta sheet fragments
+
+NC_FRAC_PAIR=x (0.3), NC_REQ_PAIR=x (0) : same for pairs of segments
+
+NSHIFT_HEL=n (3), NSHIFT_BET=n (3), NSHIFT_STRAND=n (3), NSHIFT_PAIR=n (3) :
+ allowed sequence shift to match native and compared structure for the
+ respective types of secondary structure
+
+RMS_SINGLE=n (0), CONT_SINGLE=n (1), LOCAL_SINGLE=n (1), RMS_PAIR=n (0),
+
+CONT_PAIR=n (1) : types of criteria in considering the geometry of a fragment
+ or pair native; 1 means that the criterion is turned on
+
+For nlevel > 0 (manual assignment):
+
+Level 1:
+
+1st line:
+
+NFRAG=n : number of elementary fragments
+
+Next lines (one group of lines per each fragment):
+
+1st line:
+
+NPIECE=n : number of segments constituting the fragment
+
+ANGCUT, MAXANG, FRAC_MIN, NC_FRAC, NC_REQ : criterial numbers of native-likeness
+ as for automatic classification
+
+LOCAL, ELCONT, SCCONT, RMS : types of criteria implemented, as for automatic
+ classification except that ELECONT and SCCONT mean that electrostatic or
+ side-chain contacts are considered, respectively
+
+NPIECE following lines:
+
+IFRAG1=n, IFRAG2=n : the start and end residue of a continuous segment constituting
+ a fragment
+
+Level 2 and higher:
+
+1st line:
+
+NFRAG=n : number of fragments considered at this level
+
+For each fragment the following line is read:
+
+NPIECE=n : number of elementary fragments (as defined at level 1) constituting this
+ composite fragment
+
+IPIECE=i1 i2 ... in: the numbers of these fragments
+
+NC_FRAC, NC_REQ : contact criteria (valid only for level 2)
+
+ELCONT, SCCONT, RMS : as for level 1; note, that for level 3 and higher the only
+ criterion of nativelikeness is rms
+
+3rd (for nlevel<0) or following (for n>0) line:
+
+Name of the file with reference structure (e.g., the pdb file with the
+ experimental structure)
+
+6.3. The structure of the main output file (out)
+------------------------------------------------
+
+The initial portion of the main output file, named INPUT.out_POT_000
+contains information of parameter files specified in the C-shell script,
+compilation info, and the UNRES numeric code of the amino-acid sequence.
+Subsequently, actual energy-term weights and parameter files are printed.
+If lprint was set at .true. in parmread.F, all energy-function
+parameters are printed. If REFSTR was specified in the control-data list,
+the program then outputs the read reference-structure coordinates and
+partition of structure into fragments.
+
+Subsequently, the information about the number of structures read in and
+those that were rejected is printed followed by succinct information form
+the iteration process. Finally, the histograms (also output separately to
+specific histogram files; see section 6.6) and the data of the dependence of
+free energy, energy, heat capacity, and conformational averages on temperature
+are printed (these are also output separately to file described in section
+6.6).
+
+The output files corresponding to non-master processors
+(INPUT.out_POT_xxx where xxx>0 contain only the information up to the
+iteration protocol. These files can be deleted right after the run.
+
+6.4. The thermodynamic quantity and ensemble average (thermal) files
+-----------------------------------------------------------------
+
+The files INPUT.thermal or INPUT_slice_yy.thermal contain thermodynamic,
+ensemble-averaged conformation-dependent quantities and their temperature
+derivatives. The structure of a record is as follows:
+
+ T F E q_1...q_n rmsd Rgy Cv var(q_1)...var(q_n) var(rmsd) var(Rgy) cov(q_1,E)...cov(q_n,E) cov(rmsd,E) cov(Rgy,E)
+ 298.0 -83.91454 -305.28112 0.30647 6.28347 11.61204 0.70886E+01 0.35393E-02 0.51539E+01 0.57012E+00 0.43802E+00 0.62384E+01 0.33912E+01
+
+where:
+
+T: absolute temperature (in K),
+
+F: free energy at T,
+
+E: average energy at T,
+
+q_1..q_n: ensemble-averaged q values at T (usually only the total q corresponding to whole
+ molecule is requested, as in the example above, but the user can specify
+ more than one fragment or pair of fragments for which the q's are
+ calculated, If there's no reference structure, this entry contains
+ a 0,
+
+rmsd: ensemble-averaged root mean square deviation at T,
+
+Rgy: ensemble-averaged radius of gyration computed from Calpha coordinates at T,
+
+Cv: heat capacity at T,
+
+var(q_1)...var(q_n): variances of q's at T,
+
+var(rmsd): variance of rmsd at T,
+
+var(Rgy): variance of radius of gyration at T,
+
+cov(q_1,E)...cov(q_n,E): covariances of q's and energy at T,
+
+cov(rmsd,E): covariance of rmsd and energy at T,
+
+cov(Rgy,E): covariance of radius of gyration and energy at T.
+
+According to Camacho and Thirumalali (Europhys. Lett., 35, 627, 1996), the
+maximum of the variance of the radius of gyration corresponds to the collapse
+point of a polypeptide chain and the maximum variance of q or rmsd corresponds to
+the midpoint of the transition to the native structure. More precisely, these
+points are inflection points in the plots of the respective quantities which,
+with temperature-independent force field, are proportional to their covariances
+with energy.
+
+6.5. The conformation summary with classification (stat) files
+--------------------------------------------------------------
+
+The stat files (with names INPUT_POT_xxx.stat or
+INPUT_POT_sliceyyxxx.stat; where yy is the number of a slice and xxx
+is the rank of a processor) contain the output of the classification
+of subsequent conformations (equally partitioned between processors). The
+files can be concatenated by processor rank to get a summary file. Each line
+has the following structure (example values are also provided):
+
+ | level 1 | level 2 | level3 |
+ | | | |
+ whole mol | frag1 frag2 frag3 cl1 | level3 | |
+No energy rmsd q ang dif|n1n2 n3 rms q ang rms q ang rms q ang | nc1nc2 rms q rms q cl2| rms cl3|class
+ 9999 -122.42 4.285 0.3751 47.8 |4 10 21 0.6 0.33 16.7 3.6 0.42 56.3 0.7 0.12 16.5 737 | 9 0 1.6 0.20 4.3 0.20 20 | 0 4.0 2 |737.20.2
+
+No - number of conformation
+
+whole mol denotes the characteristics of the whole molecule
+q - 1-(Wolynes' q)
+
+level 1, 2, and 3 denote the characteristics computed for the respective fragments
+as these levels.
+
+n1, n2, n3 - number of native contacts for a given segment
+
+cl1, cl2, cl3 - group of segment classes for segments at level 1, 2, and 3, respectively
+
+class - total class of the conformation
+
+The octal/quaternary/binary numbers denoting the class for a fragment at level 1, 2,
+and 3, respectively, are described in ref. 3
+
+6.6. The histogram files
+------------------------
+
+The histogram file with names INPUT_[par_yy][_slice_xx].hist where xx denotes
+the number of the slice and yy denotes the number of the parameter if
+SEPARATE_PARSET was specified in input contain histograms of q at replica
+temperatures and energy-parameter sets; with SEPARATE_PARSET histograms
+corresponding to subsequent parameter sets are saved in files with par_yy
+infixes. The histograms are multidimensional if q is a vector (usually,
+however, q corresponds to the entire molecule and, consequently, the
+histograms are one-dimensional). The histogram files are printed if histfile
+and histout was specified in the control data record.
+
+Each line of a histogram file corresponds to a given (multidimensional) bin in
+q contains the following:
+
+q_1,...,q_n at a given bin (format f6.3 for each)
+
+histogram values for subsequent replica temperatures (format e20.10 for each)
+
+iparm (the number of parameter set; format i5)
+
+If SEPARATE_PARSET was not specified, the entries corresponding to each
+parameter follow one another.
+
+The state density (microcanonical entropy) is printed to file(s)
+INPUT[_slice_xx].ent. Each line contains the left boundary of the energy
+bin and ln(state density) followed by " ent" string. At present, the state
+density is calculated correctly only if one energy-parameter set is used.
+
+6.7. The rmsd-radius of gyration potential of mean force files
+------------------------------------------
+
+These files with names INPUT[_par_yy][_slice_xx].rmsrgy contain the
+two-dimensional potentials of mean force in rmsd and radius of gyration
+at all replica-exchange temperatures and for all energy-parameter sets.
+A line contains the left boundaries of the radius of gyration - rmsd bin
+(radius of gyration first) (format 2f8.2) and the PMF values at all
+replica-exchange temperatures (e14.5), followed by the number of the parameter
+set. With SEPARATE_PARSET, the PMFs corresponding to different parameter sets
+are printed to separate files.
+
+6.8. The PDB files
+------------------
+
+The PDB files with names INPUT_[slice_xx_]Tyyy.pdb, where Tyyy specifies
+a given replica temperature contain the conformations whose probabilities at
+replica temperature T sum to 0.99, after sorting the conformations by
+probabilities in descending order. The PDB files follow the standard format;
+see ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf.
+For single-chain proteins, an example is as follows:
+
+REMARK CONF 9059 TEMPERATURE 330.0 RMS 8.86
+REMARK DIMENSIONLESS FREE ENERGY -1.12726E+02
+REMARK ENERGY -2.22574E+01 ENTROPY -7.87818E+01
+ATOM 1 CA VAL 1 8.480 5.714 -34.044
+ATOM 2 CB VAL 1 9.803 5.201 -33.968
+ATOM 3 CA ASP 2 8.284 2.028 -34.925
+ATOM 4 CB ASP 2 7.460 0.983 -33.832
+.
+.
+.
+ATOM 115 CA LYS 58 28.446 -3.448 -12.936
+ATOM 116 CB LYS 58 26.613 -4.175 -14.514
+TER
+CONECT 1 3 2
+.
+.
+.
+CONECT 113 115 114
+CONECT 115 116
+
+where
+
+CONF is the number of the conformation from the processed slice of MREMD
+trajectories
+
+TEMPERATURE is the replica temperature
+
+RMS is the Calpha rmsd from the reference (experimental) structure.
+
+DIMENSIONLESS FREE ENERGY is -log(probability) (equation 14 of ref 2)
+for the conformation at this replica temperature calculated by WHAM.
+
+ENERGY is the UNRES energy of the conformation at the replica temperature
+(note that UNRES energy is in general temperature dependent).
+
+ENTROPY is the omega of equation 15 of ref 2 of the conformation
+
+In the ATOM entries, CA denotes a Calpha atom and CB denotes UNRES side-chain
+atom. The CONECT entries specify the Calpha(i)-Calpha(i-1),
+Calpha(i)-Calpha(i+1) and Calpha(i)-SC(i) links.
+
+The PDB files generated for oligomeric proteins are similar except that
+chains are separated with TER and molecules with ENDMDL records and chain
+identifiers are included. An example is as follows:
+
+REMARK CONF 765 TEMPERATURE 301.0 RMS 11.89
+REMARK DIMENSIONLESS FREE ENERGY -4.48514E+02
+REMARK ENERGY -3.58633E+02 ENTROPY 1.51120E+02
+ATOM 1 CA GLY A 1 -0.736 11.305 24.600
+ATOM 2 CA TYR A 2 -3.184 9.928 21.998
+ATOM 3 CB TYR A 2 -1.474 10.815 20.433
+.
+.
+.
+ATOM 40 CB MET A 21 -4.033 -2.913 27.189
+ATOM 41 CA GLY A 22 -5.795 -10.240 27.249
+TER
+ATOM 42 CA GLY B 1 6.750 -6.905 19.263
+ATOM 43 CA TYR B 2 5.667 -4.681 16.362
+.
+.
+.
+ATOM 163 CB MET D 21 4.439 12.326 -4.950
+ATOM 164 CA GLY D 22 10.096 14.370 -9.301
+TER
+CONECT 1 2
+CONECT 2 4 3
+.
+.
+.
+CONECT 39 41 40
+CONECT 42 43
+.
+.
+.
+CONECT 162 164 163
+ENDMDL
+
+6.8. The compressed Cartesian coordinates (cx) files
+----------------------------------------------------
+
+These files contain compressed data in the Europort Data Compression XDRF
+library format written by Dr. F. van Hoesel, Groeningen University
+(http://hpcv100.rc.rug.nl/xdrfman.html). The files are written
+by the cxwrite subroutine. The resulting cx file contains the omega
+factors to compute probabilities of conformations at any temperature
+and any energy-function parameters if Hamiltonian replica exchange was
+performed in the preceding UNRES run. The files have general names
+INPUT[_par_yy][_slice_xx].cx where xx is slice number and yy is parameter-set
+number.
+
+The items written to the cx file are as follows (the precision is 5
+significant digits):
+
+1) Cartesian coordinates of Calpha and SC sites
+2) nss (number of disulfide bonds)
+3) if nss > 0:
+ a) ihpb (first residue of a disulfide link)
+ b) jhpb (second residue of a disulfide link)
+4) UNRES energy at that replica temperature that the conformation was at
+ snapshot-recording time,
+5) ln(omega) of eq 15 of ref 2,
+6) Calpha rmsd
+7) conformation class number (0 if CLASSIFY was not specified).
+
+7. SUPPORT
+----------
+
+ Dr. Adam Liwo
+ Faculty of Chemistry, University of Gdansk
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.
+ phone: +48 58 523 5430
+ fax: +48 58 523 5472
+ e-mail: adam@chem.univ.gda.pl
+
+ Dr. Cezary Czaplewski
+ Faculty of Chemistry, University of Gdansk
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.
+ phone: +48 58 523 5430
+ fax: +48 58 523 5472
+ e-mail: czarek@chem.univ.gda.pl
+
+Prepared by Adam Liwo, 02/19/12
--- /dev/null
+ XDRF2PDB, XDRF2PDB-M, XDRF2X - programs to convert compressed
+ Cartesian coordinate files from UNRES into ASCII formats
+ ------------------------------------------------------------
+
+TABLE OF CONTENTS
+-----------------
+
+1. License terms
+
+2. Programs and their functions
+
+3. Installation
+
+4. Command lines and files
+ 4.1 xdrf2pdb
+ 4.2 xdrf2pdb-m
+ 4.3 xdrf2x
+ 4.4 xdrf2ang
+
+5. Support
+
+1. LICENSE TERMS
+----------------
+
+* This software is provided free of charge to academic users, subject to the
+ condition that no part of it be sold or used otherwise for commercial
+ purposes, including, but not limited to its incorporation into commercial
+ software packages, without written consent from the authors. For permission
+ contact Prof. H. A. Scheraga, Cornell University.
+
+* This software package is provided on an "as is" basis. We in no way warrant
+ either this software or results it may produce.
+
+* Reports or publications using this software package must contain an
+ acknowledgment to the authors and the NIH Resource in the form commonly
+used
+ in academic research.
+
+2. PROGRAMS AND THEIR FUNCTONS
+------------------------------
+
+The following three programs can be used to extract conformations from
+compressed Cartesian (cx) files from UNRES:
+
+xdrf2pdb - takes a single trajectory file and converts it into PDB format.
+
+xdrf2pdb-m - takes a multiple-trajectory file from UNRES/MREMD simulations
+ and enables the user to extract conformation of a particular
+ trajectory and save them to a PDB file.
+
+xdrf2x - takes a single trajectory file and converts it into UNRES Cartesian
+ coordinate (x) format
+
+xdrf2ang - takes a single trajectory file and calculates UNRES backbone
+ angles (theta and gamma).
+
+3. INSTALLATION
+---------------
+
+Run make all on your system to install all programs or make <program>
+to install a particular program. You might need to run make in the
+xdrf subdirectory beforehand or point to the xdrf library that is on another
+directory in the Makefile.
+
+The program compiles on all known Fortran compilers, including gfortran.
+
+4. COMMAND LINE AND FILES
+-------------------------
+
+For xdrf2pdb and xdrf2pdb-m, you'll need to prepare the UNRES sequence file
+in either one- or three-letter code.
+
+4.1 XDRF2PDB
+
+Command line syntax:
+
+xdrf2pdb one/three seqfile cxfile [freq] [start] [end] [pdbfile]
+
+where
+
+one or three indicates in what format the sequence will be read
+
+seqfile - the file with the sequence:
+
+one-letter format: 80A1
+
+three-letter format: 20(A3,1X)
+
+Note that the sequence must match exactly the UNRES sequence
+
+cxfile - full name of the trajectory file with compressed Cartesian coordinates.
+
+freq (1) - conformation sampling frequency (each freq-th conformation will
+ be saved to PBD file
+
+start (1) - the first conformation to be saved to PDB file
+
+end (1000000000) the last conformation to be saved to PDB file
+
+pdbfile (cxfile with extension changed from cx to pdb) - the output PDB file
+
+4.2 XDRF2PDB-M
+
+Command line syntax:
+xdrf2pdb-m xdrf2pdb-m one/three seqfile cxfile ntraj itraj [pdbfile] [freq]
+
+cxfile - the name of the compressed trajectory file from an UNRES/MREMD run
+ carried out with TRAJ1FILE (conformations from all trajectories
+ output to a single file)
+
+ntraj - number of trajectories in the multi-trajectory run
+
+itraj - the number of trajectory to be extracted
+
+pdbfile - (cxfile-without-cx-itraj.pdb) the name of file to write the Cartesian
+ coordinates of trajectory itraj to
+
+freq (1) - output frequency
+
+The xdrf2pdb program to convert cx files to pdb files
+
+The source is in xdrf2pdb; it requires the libraries in xdrf
+
+4.3 XDRF2X
+
+Command line syntax:
+
+xdrf2x cxfile [is] [ie] [freq] > x_file
+
+The meaning of the the arguments is as in section 4.1; the conformations
+are output in UNRES Cartesian coordinate format to stdout.
+
+4.4. XDRF2ANG
+
+Command line syntax:
+
+xdrf2ang one/three seqfile cxfile [freq] [start] [end] [angfile]
+
+The meaning of the first six parameters is as in section 4.1; angfile is
+the name of the output angle file; is assigned cx file name with the cx
+extension changed to ang, if not present.
+
+5. SUPPORT
+----------
+
+ Dr. Adam Liwo
+ Faculty of Chemistry, University of Gdansk
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.
+ phone: +48 58 523 5430
+ fax: +48 58 523 5472
+ e-mail: adam@chem.univ.gda.pl
+
+ Dr. Cezary Czaplewski
+ Faculty of Chemistry, University of Gdansk
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.
+ phone: +48 58 523 5430
+ fax: +48 58 523 5472
+ e-mail: czarek@chem.univ.gda.pl
+
+Prepared by Adam Liwo, 11/26/11
--- /dev/null
+\documentclass[12pt]{article}
+%\usepackage{latex2html}
+\usepackage{enumerate}
+\usepackage{longtable}
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{color}
+\parindent=0pt
+\parskip=12pt
+\textheight=24cm
+\textwidth=18cm
+\topmargin=-2.5cm
+\oddsidemargin=-0.5cm
+\setcounter{secnumdepth}{5}
+\setcounter{tocdepth}{5}
+\begin{document}
+\sloppy
+
+\title{CLUSTER\\
+Cluster analysis of UNRES simulation results}
+
+\author{Department of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Sobieskiego 18\\ 80-952 Gdansk, Poland\\
+\\
+\\
+Scheraga Group\\ Baker Laboratory of Chemistry \\
+and Chemical Biology\\ Cornell University\\ Ithaca, NY 14853-1303, USA}
+
+\maketitle
+
+\newpage
+
+\tableofcontents
+
+% 1. License terms
+% 2. References
+% 3. Functions of the program
+% 4. Installation
+% 5. Running the program
+% 6. Input and output files
+% 6.1. Summary of files
+% 6.2. The main input file
+% 6.2.1. Title
+% 6.2.2. General data
+% 6.2.3. Energy-term weights and parameter files
+% 6.2.4 Molecule data
+% 6.2.4.1. Sequence information
+% 6.2.4.2. Dihedral angle restraint information
+% 6.2.4.3. Disulfide-bridge data
+% 6.2.5. Reference structure
+% 6.3. Main output file (out)
+% 6.4. Output coordinate files
+% 6.4.1. The internal coordinate (int) files
+% 6.4.2. The Cartesian coordinate (x) files
+% 6.4.3. The PDB files
+% 6.4.3.1. CLUST-UNRES runs
+% 6.4.3.2. CLUST-WHAM runs
+% 6.4.3.2.1. Conformation family files
+% 6.4.3.2.2. Average-structure file
+% 6.5. The conformation-distance file
+% 6.6. The clustering-tree PicTeX file
+% 7. Support
+
+\newpage
+
+\section{LICENSE TERMS}
+\label{sect:license}
+
+\begin{itemize}
+
+\item
+ This software is provided free of charge to academic users, subject to the condition that no part of it be sold or used otherwise for commercial purposes, including, but not limited to its incorporation into commercial software packages, without written consent from the authors. For permission contact Prof. H. A. Scheraga, Cornell University.
+
+\item
+ This software package is provided on an ``as is'' basis. We in no way warrant either this software or results it may produce.
+
+\item
+ Reports or publications using this software package must contain an acknowledgment to the authors and the NIH Resource in the form commonly used in academic research.
+
+\end{itemize}
+
+\newpage
+
+\section{REFERENCES}
+\label{sect:references}
+
+The program incorporates the hierarchical-clustering subroutine, hc.f written
+by G. Murtagh (refs 1 and 2). The subroutine contains seven methods of
+hierarchical clustering.
+
+\begingroup
+\renewcommand{\section}[2]{}%
+\begin{thebibliography}{10}
+
+\bibitem{murtagh_1985}
+Murtagh. Multidimensional clustering algorithms; Physica-Verlag:
+Vienna, Austria, 1985.
+
+\bibitem{murtagh_1987}
+F. Murtagh, A. Heck. MultiVariate data analysis; Kluwer Academic:
+Dordrecht, Holland, 1987.
+
+\bibitem{liwo_2007}
+A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, K. Wachucik,
+H.A. Scheraga.
+Modification and optimization of the united-residue (UNRES) potential
+energy function for canonical simulations. I. Temperature dependence of the
+effective energy function and tests of the optimization method with single
+training proteins. {\it J. Phys. Chem. B}, {\bf 2007}, 111, 260-285.
+
+\bibitem{oldziej_2004}
+S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+Optimization of the UNRES force field by hierarchical design of the
+potential-energy landscape. 2. Off-lattice tests of the method with single
+proteins. {\it J. Phys. Chem. B.}, {\bf 2004}, 108, 16934-16949.
+
+\end{thebibliography}
+\endgroup
+
+\newpage
+
+\section{FUNCTIONS OF THE PROGRAM}
+\label{sect:functions}
+
+The program runs cluster analysis of UNRES simulation results. There are two
+versions of the program depending on the origin of input conformation:
+
+\begin{enumerate}
+
+\item
+ CLUST-UNRES: performs cluster analysis of conformations that are obtained
+ directly from UNRES runs (CSA, MCM, MD, (M)REMD, multiple-conformation
+ energy minimization). The source code and other important files are
+ deposited in CLUST-UNRES subdirectory
+
+ The source code of this version is deposited in clust-unres/src
+
+\item
+ CLUST-WHAM: performs cluster analysis of conformations obtained in UNRES
+ MREMD simulations and then processed with WHAM (weighted histogram analysis
+ method). This enables the user to obtain clusters as conformational
+ ensembles at a given temperature and to compute their probabilities
+ (section 2.5 of ref 3). This version is deposited in the CLUST-WHAM
+ subdirectory. This version has single- and multichain variants, whose
+ source codes are deposited in the following subdirectories:
+
+\begin{enumerate}
+
+\item
+ clust-wham/src single-chain proteins
+
+\item
+ clust-wham/src-M oligomeric proteins
+
+\end{enumerate}
+
+\end{enumerate}
+
+The version developed for oligomeric proteins treats whole system as a single
+chain with dummy residues inserted. It also works for single chains but is
+not fully checked and it is recommended to use single-chain version for
+single-chain proteins.
+
+\section{INSTALLATION}
+\label{sect:install}
+
+Customize Makefile to your system. See section 7 of the description of UNRES
+for compiler flags that are used to created executables for a particular
+force field. There are already several Makefiles prepared for various
+systems and force fields.
+
+Run make in the appropriate source directory version. CLUST-UNRES runs
+only in single-processor mode an CLUST-WHAM runs in both serial and parallel
+mode [only conformation-distance (rmsd) calculations are parallelized].
+The parallel version uses MPI.
+
+\section{RUNNING THE PROGRAM}
+\label{sect:running}
+
+The program requires a parallel system to run. Depending on system,
+either the wham.csh C-shell script (in WHAM/bin directory) can be started
+using mpirun or the binary in the C-shell script must be executed through
+mpirun. See the wham.csh C-shell script and section 6 for the files
+processed by the program.
+
+\newpage
+
+\section{INPUT AND OUTPUT FILES}
+\label{sect:inoutfiles}
+
+\subsection{Summary of files}
+\label{sect:inoutfiles:summary}
+
+The C-shell script wham.csh is used to run the program (see the
+bin/WHAM directory). The data files that the script needs are mostly the same as
+for UNRES (see section 6 of UNRES description). In addition, the environmental
+variable CONTFUN specifies the method to assess whether two side chains
+are at contact; if EONTFUN=GB, the criterion defined by eq 8 of ref 4 is
+used to assess whether two side chains are at contact. Also, the parameter
+files from the C-shell scripts are overridden if the data from Hamiltonian
+MREMD are processed; if so, the parameter files are defined in the main
+input file.
+
+The main input file must have inp extension. If it is INPUT.inp, the output
+files are as follows:
+
+Coordinate input file COORD.ext, where ext denotes file extension in one of the
+following formats:
+
+\begin{description}
+\item{int} (extension int; UNRES angles theta, gamma, alpha, and beta),
+\item{x} (extension x; UNRES Cartesian coordinate format; from MD),
+\item{pdb} (extension pdb; Protein Data Bank format; fro MD),
+\item{cx} (extension cx; xdrf format; from WHAM).
+\end{description}
+
+\begin{description}
+\item{INPUT\_clust.out} (single-processor mode) or INPUT\_clust.out\_xxx (parallel mode) --
+ output file(s) (INPUT.out\_000 is the main output file for parallel mode).
+
+\item{COORD\_clust.int} -- leading (lowest-energy) members of the families.
+ in internal-coordinate format.
+\item{COORD\_clust.x} -- leading members of the families in UNRES Cartesian coordinate
+ format.
+\item{COORD\_xxxx.pdb} or COORD\_xxxx\_yyy.pdb (CLUST-UNRES) -- PDB file of member yyy
+ of family xxxx; yyy is omitted if the family contains only one member
+ within a given energy cut-off.
+\item{COORD\_TxxxK\_yyyy.pdb} -- concatenated conformations in PDB format of the
+ members of family yyyy clustered at T=xxxK ranked by probabilities in
+ descending order at this temperature (CLUST-WHAM).
+\item{COORD\_T\_xxxK\_ave.pdb} -- cluster-averaged coordinates and coordinates of a
+ member of each family that is closest to the cluster average in PDB
+ format, concatenated in a single file (CLUST-WHAM).
+
+\item{INPUT\_clust.tex} -- PicTeX code of the cluster tree.
+
+\item{INPUT.rms} -- rmsds between conformations.
+
+\end{description}
+
+\subsection{Main input file}
+\label{sect:inoutfiles:main}
+
+This file has the same structure as the UNRES input file; most of the data are
+input in a keyword-based form (see section 7.1 of UNRES description). The data
+are grouped into records, referred to as lines. Each record, except for the
+records that are input in non-keyword based form, can be continued by placing
+an ampersand (\&) in column 80. Such a format is referred to as the data list
+format.
+
+In the following description, the default values are given in parentheses.
+
+\subsubsection{Title}
+
+An 80-character string from the first line is input.
+
+\subsubsection{General data}
+\label{sect:inoutfiles:main:general}
+
+(Data list format.)
+
+\begin{description}
+
+\item{NRES} (0) -- the number of residues.
+
+\item{ONE\_LETTER} -- if present, the sequence is input in one-letter code.
+
+\item{SYM} (1) -- number of chains with same sequence (for oligomeric proteins only).
+
+\item{WITH\_DIHED\_CONSTR} -- if present, dihedral-angle restraints were imposed in the
+ processed MREMD simulations
+
+\item{RESCALE} (1) -- Choice of the type of temperature dependence of the force field.
+
+\begin{description}
+\item{0} -- no temperature dependence,
+\item{1} -- homographic dependence (not implemented yet with any force field)
+\item{2} -- hyperbolic tangent dependence \cite{liwo_2007}.
+\end{description}
+
+\item{DISTCHAINMAX} (50.0) -- for oligomeric proteins, distance between the chains
+ above which restraints will be switched on to keep the chains at a
+ reasonable distance.
+
+\item{PDBOUT} -- clusters will be printed in PDB format.
+
+\item{ECUT} -- energy cut-off criterion to print conformations (UNRES-CLUST runs).
+ Only those families will be output the energy of the lowest-energy
+ conformation of which is within ECUT kcal/mol above that of the
+ lowest-energy conformation and for a family only those members will be
+ output which have energy within ECUT kcal/mol above the energy of the
+ lowest-energy member of the family.
+
+\item{PRINT\_CART} -- output leading members of the families in UNRES x format.
+
+\item{PRINT\_INT} -- output leading members of the families in UNRES int format.
+
+\item{REF\_STR} -- if present, reference structure is input and rmsd will be computed
+ with respect to it (CLUST-UNRES only; rmsd is provided in the cx file
+ from WHAM for CLUST-WHAM runs).
+
+\item{PDBREF} -- if present, reference structure will be read in from a pdb file.
+
+\item{SIDE} -- side chains will be considered in superposition when calculating rmsd.
+
+\item{CA\_ONLY} -- only the Calpha atoms will be used in rmsd calculation.
+
+\item{NSTART} (0) -- first residue to superpose.
+
+\item{NEND} (0) -- last residue to superpose.
+
+\item{NTEMP} (1) -- number of temperatures at which probabilities will be calculated
+ and clustering performed (CLUST-WHAM).
+
+\item{TEMPER} (NTEMP tiles) -- temperatures at which clustering will be performed
+ (CLUST-WHAM).
+
+\item{EFREE} -- if present, conformation entropy factor is read if the conformation
+ is input from an x or pdb file.
+
+\item{PROB} (0.99) -- cut-off on the summary probability of the conformations that
+ are clustered at a given temperature (CLUST-WHAM).
+
+\item{IOPT} (2) - clustering algorithm:
+
+\begin{description}
+\item{1} -- Ward's minimum variance method.
+\item{2} -- single link method.
+\item{3} -- complete link method.
+\item{4} -- average link (or group average) method.
+\item{5} -- McQuitty's method.
+\item{6} -- Median (Gower's) method.
+\item{7} -- centroid method.
+\end{description}
+
+Instead of IOPT=1, MINTREE and instead of IOPT=2 MINVAR can be specified
+
+\item{NCUT} (1) -- number of cut-offs in clustering.
+
+\item{CUTOFF} (-1.0; NCUT values) cut-offs at which clustering will be performed;
+ at the cut-off flagged by a ``-'' sign clustering will be performed with
+ cutoff value=abs(cutoff(i)) and conformations corresponding to clusters
+ will be output in the desired format.
+
+\item{MAKE\_TREE} -- if present, produce a clustering-tree graph.
+
+\item{PLOT\_TREE} -- if present, the tree is written in PicTeX format to a file.
+
+\item{PRINT\_DIST} -- if present, distance (rmsd) matrix is printed to main output
+ file.
+
+\item{PUNCH\_DIST} -- if present, the upper-triangle of the distance matrix will be
+ printed to a file.
+\end{description}
+
+\subsubsection{Energy-term weights and parameter files}
+\label{sect:inoutfiles:main:weights}
+
+\begin{description}
+\item{WSC (1.0)} -- side-chain-side-chain interaction energy.
+
+\item{WSCP} (1.0) -- side chain-peptide group interaction energya.
+
+\item{WELEC} (1.0) -- peptide-group-peptide group interaction energy.
+
+\item{WEL\_LOC} (1.0) -- third-order backbone-local correlation energy.
+
+\item{WCORR} (1.0) -- fourth-order backbone-local correlation energy.
+
+\item{WCORR5} (1.0) -- fifth-order backbone-local correlation energy.
+
+\item{WCORR6} (1.0) -- sixth-order backbone-local correlation energy.
+
+\item{WTURN3} (1.0) -- third-order backbone-local correlation energy of pairs of
+ peptide groups separated by a single peptide group.
+
+\item{WTURN4} (1.0) -- fourth-order backbone-local correlation energy of pairs of
+ peptide groups separated by two peptide groups.
+
+\item{WTURN6} (1.0) -- sixth-order backbone-local correlation energy for pairs of
+ peptide groups separated by four peptide groups.
+
+\item{WBOND} (1.0) -- virtual-bond-stretching energy.
+
+\item{WANG} (1.0) -- virtual-bond-angle-bending energy.
+
+\item{WTOR} (1.0) -- virtual-bond-torsional energy.
+
+\item{WTORD} (1.0) -- virtual-bond-double-torsional energy.
+
+\item{WSCCOR} (1.0) -- sequence-specific virtual-bond-torsional energy.
+
+\item{WDIHC} (0.0) -- dihedral-angle-restraint energy.
+
+\item{WHPB} (1.0) -- distance-restraint energy.
+
+\item{SCAL14} (0.4) -- scaling factor of 1,4-interactions
+
+\end{description}
+
+\subsubsection{Molecule information}
+\label{sect:inoutfiles:main:molinfo}
+
+\paragraph{Sequence information\\ \\}
+\label{sect:inoutfiles:main:molinfo:sequence}
+
+Amino-acid sequence
+
+3-letter code: Sequence is input in format 20(1X,A3)
+
+1-letter code: Sequence is input in format 80A1
+
+\paragraph{Dihedral angle restraint information\\ \\}
+\label{sect:inoutfiles:molinfo:dihrestr}
+
+This is the information about dihedral-angle restraints, if any are present.
+It is specified only when WITH\_DIHED\_CONSTR is present in the first record.
+
+1st line: ndih\_constr -- number of restraints (free format)
+
+2nd line: ftors -- force constant (free format)
+
+Each of the following ndih\_constr lines:
+
+idih\_constr(i),phi0(i),drange(i) (free format)
+
+\begin{description}
+\item{idih\_constr(i)} -- the number of the dihedral angle gamma corresponding to the
+ith restraint
+
+\item{phi0(i)} -- center of dihedral-angle restraint
+
+\item{drange(i)} -- range of flat well (no restraints for phi0(i) +/- drange(i))
+
+\end{description}
+
+\paragraph{Disulfide-bridge data \\ \\}
+\label{sect:inoutfiles:molinfo:disulfide}
+
+1st line: NS, (ISS(I),I=1,NS) (free format)
+
+\begin{description}
+
+\item{NS} -- number of cystine residues forming disulfide bridges.
+
+\item{ISS(I)} -- the number of the Ith disulfide-bonding cystine in the sequence.
+
+\end{description}
+
+2nd line: NSS, (IHPB(I),JHPB(I),I=1,NSS) (free format)
+
+\begin{description}
+
+\item{NSS} -- number of disulfide bridges
+
+\item{IHPB(I),JHPB(I)} -- the first and the second residue of ith disulfide link.
+
+Because the input is in free format, each line can be split
+\end{description}
+
+\subsubsection{Reference structure}
+\label{sect:inoutfiles:molinfo:refstr}
+
+If PDBREF is specified, filename with reference (experimental) structure,
+otherwise UNRES internal coordinates as the theta, gamma, alpha, and beta
+angles.
+
+\subsection{Main output file}
+\label{sect:inoutfiles:mainoutput}
+
+The main (with name INPUT\_clust.out or INPUT\_clust.out\_000 for parallel runs)
+output file contains the results of clustering (numbers of families
+at different cut-off values, probabilities of clusters, composition of
+families, and rmsd values corresponding to families (0 if rmsd was not
+computed or read from WHAM-generated cx file).
+
+The output files corresponding to non-master processors
+(INPUT\_clust.out\_xxx where xxx$>$0 contain only the information up to the
+clustering protocol. These files can be deleted right after the run.
+
+Excerpts from the a sample output file are given below:
+
+CLUST-UNRES:
+
+\begin{verbatim}
+
+THERE ARE 20 FAMILIES OF CONFORMATIONS
+
+FAMILY 1 CONTAINS 2 CONFORMATION(S):
+ 42 -2.9384E+03 50 -2.9134E+03
+
+
+Max. distance in the family: 14.0; average distance in the family: 14.0
+
+FAMILY 2 CONTAINS 3 CONFORMATION(S):
+ 13 -2.9342E+03 7 -2.8827E+03 10 -2.8682E+03
+\end{verbatim}
+
+CLUST-WHAM:
+
+\begin{verbatim}
+AT CUTOFF: 200.00000
+Maximum distance found: 137.82
+Free energies and probabilities of clusters at 325.0 K
+clust efree prob sumprob
+ 1 -76.5 0.25035 0.25035
+ 2 -76.5 0.24449 0.49484
+ 3 -76.4 0.21645 0.71129
+ 4 -76.4 0.20045 0.91174
+ 5 -75.8 0.08826 1.00000
+
+
+THERE ARE 5 FAMILIES OF CONFORMATIONS
+
+FAMILY 1 WITH TOTAL FREE ENERGY -7.65228E+01 CONTAINS 548 CONFORMATION(S):
+8363 -7.332E+013939 -7.332E+012583 -7.332E+017395 -7.332E+019932 -7.332E+01
+5816 -7.332E+013096 -7.332E+012663 -7.332E+014099 -7.332E+016822 -7.332E+01
+3176 -7.332E+017542 -7.332E+018933 -7.332E+017315 -7.332E+01 200 -7.332E+01.
+.
+5637 -7.062E+018060 -7.061E+013797 -7.060E+018800 -7.057E+016295 -7.057E+01
+6298 -7.057E+012332 -7.057E+012709 -7.057E+01
+
+Max. distance in the family: 16.5; average distance in the family: 8.8
+Average RMSD 8.22 A
+\end{verbatim}
+
+\subsection{Output coordinate files}
+\label{sect:inoutfiles:outcoord}
+
+\subsubsection{The internal coordinate (int) files}
+\label{sect:inoutfiles:int}
+
+The file with name COORD\_clust.int contains the angles theta, gamma, alpha,
+and beta of all residues of the leaders (lowest UNRES energy conformations
+from consecutive families for CLUST-UNRES runs and lowest free energy
+conformations for CLUST-WHAM runs). The format is the same as that of the
+file output by UNRES; see section 9.1.1 of UNRES description.
+
+For CLUST-WHAM runs, the first line contains more items:
+
+\begin{tabular}{ll}
+number of family &(format i5)\\
+UNRES free energy of the conformation &(format f12.3)\\
+Free energy of the entire family &(format f12.3)\\
+number of disulfide bonds &(format i2)\\
+list disulfide-bonded pairs &(format 2i3)\\
+conformation class number (0 if not provided)&(format i10)\\
+\end{tabular}
+
+\subsubsection{The Cartesian coordinate (x) files}
+\label{sect:inoutfiles:card}
+
+The file with name COORD\_clust.x contains the Cartesian coordinates of the
+alpha-carbon and side-chain-center coordinates. The coordinate format is
+as in section 9.1.2 of UNRES description and the first line contains the
+following items:
+
+\begin{tabular}{ll}
+Number of the family &(format I5)\\
+UNRES free energy of the conformation &(format f12.3)\\
+Free energy of the entire family &(format f12.3)\\
+number of disulfide bonds &(format i2)\\
+list disulfide-bonded pairs &(format 2i3)\\
+conformation class number (0 if not provided)&(format i10)\\
+\end{tabular}
+
+\subsubsection{The PDB files}
+\label{sect:inoutfiles:PDB}
+
+The PDB files are in standard format (see
+\href{ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf}{ftp://ftp.wwpdb.org/pub/pdb/doc/format\_descriptions}).
+The ATOM records contain Calpha coordinates (CA) or UNRES side-chain-center
+coordinates (CB). For oligomeric proteins chain identifiers are present
+(A, B, ..., etc.) and each chain ends with a TER record. Coordinates of a
+single conformation or multiple conformations The header (REMARK) records
+and the contents depends on cluster run type. The next subsections are devoted
+to different run types.
+
+\paragraph{CLUST-UNRES runs \\ \\}
+\label{sect:inoutfiles:PDB:clust-unres}
+
+The files contain the members of the families obtained from clustering such
+that the lowest-energy conformation of a family is within ECUT kcal/mol higher
+in energy than the lowest-energy conformation. Again, within a family, only
+those conformations are output whose energy is within ECUT kcal/mol above
+that of the lowest-energy member of the family. Families and the members
+of a family within a family are ranked by increasing energy. The file names are:
+
+COORD\_xxxx.pdb where xxxx is the number of the family, if the family contains
+ only one member of if only one member is output.
+
+COORD\_xxxx\_yyy.pdb where xxxx is the number of the family and yyy is the number
+ of the member of this family.
+
+An example is the following:
+
+\begin{verbatim}
+REMARK R0001 ENERGY -2.93843E+03
+ATOM 1 CA GLY 1 0.000 0.000 0.000
+ATOM 2 CA HIS 2 3.800 0.000 0.000
+ATOM 3 CB HIS 2 5.113 1.656 0.015
+ATOM 4 CA VAL 3 5.927 -3.149 0.000
+.
+.
+.
+ATOM 346 CB GLU 183 -43.669 -32.853 -7.320
+TER
+CONECT 1 2
+CONECT 2 4 3
+.
+.
+.
+CONECT 341 343 342
+CONECT 343 344
+CONECT 345 346
+\end{verbatim}
+
+where ENERGY is the UNRES energy. The CONECT records defined the Calpha-Calpha
+and Calpha-SC connection.
+
+\paragraph{CLUST-WHAM runs\\ \\}
+\label{sect:inoutfiles:PDB:clust-wham}
+
+The program generates a file for each family with its members and a summary
+file with ensemble-averaged conformations for all families. These are described
+in the two next sections.
+
+\subparagraph{Conformation family files\\ \\}
+\label{sect:inoutfiles:PDB:clust-unres:family}
+
+For each family, the file name is COORD\_TxxxK\_yyyy.pdb, where yyyy is the
+number of the family and xxx is the integer part of the temperature (K).
+The first REMARK line in the file contains the information about the free
+energy and average rmsd of the entire cluster and, for each conformation,
+the initial REMARK line contains these quantities for this conformation.
+Same applies to oligomeric proteins, for which the TER records separate the
+chains and the ENDMDL record separates conformations.
+An example is given below.
+
+\begin{verbatim}
+REMARK CLUSTER 1 FREE ENERGY -7.65228E+01 AVE RMSD 8.22
+REMARK 1BDD L18G full clust ENERGY -7.33241E+01 RMS 10.40
+ATOM 1 CA VAL 1 18.059 -33.585 4.616 1.00 5.00
+ATOM 2 CB VAL 1 18.720 -32.797 3.592 1.00 5.00
+.
+.
+.
+ATOM 115 CA LYS 58 29.641 -44.596 -8.159 1.00 5.00
+ATOM 116 CB LYS 58 27.593 -45.927 -8.930 1.00 5.00
+TER
+CONECT 1 3 2
+CONECT 3 5 4
+.
+.
+CONECT 113 114
+CONECT 115 116
+TER
+REMARK 1BDD L18G full clust ENERGY -7.33240E+01 RMS 10.04
+ATOM 1 CA VAL 1 3.174 2.833 -34.386 1.00 5.00
+ATOM 2 CB VAL 1 3.887 2.811 -33.168 1.00 5.00
+.
+.
+ATOM 115 CA LYS 58 16.682 6.695 -20.438 1.00 5.00
+ATOM 116 CB LYS 58 18.925 5.540 -20.776 1.00 5.00
+TER
+CONECT 1 3 2
+CONECT 3 5 4
+CONECT 113 114
+CONECT 115 116
+TER
+\end{verbatim}
+
+\subparagraph{Average-structure file\\ \\}
+\label{sect:inoutfiles:PDB:clust-unres:average}
+
+The file name is COORD\_T\_xxxK\_ave.pdb. The entries are in pairs; the first
+one is cluster-averaged conformation and the second is a family member which
+has the lowest rmsd from this average conformation. Computing average
+conformations is explained in section 2.5 of ref 3. Example excerpts from
+an entry corresponding to a given family are shown below.
+
+\begin{verbatim}
+REMAR AVERAGE CONFORMATIONS AT TEMPERATURE 300.00
+REMARK CLUSTER 1
+REMARK 2HEP clustering 300K ENERGY -8.22572E+01 RMS 3.29
+ATOM 1 CA MET 1 -17.748 48.148 -19.284 1.00 5.96
+ATOM 2 CB MET 1 -17.373 47.911 -19.294 1.00 6.34
+ATOM 3 CA ILE 2 -18.770 49.138 -18.133 1.00 3.98
+.
+.
+.
+ATOM 80 CB PHE 41 -14.353 44.680 -15.642 1.00 2.62
+ATOM 81 CA ARG 42 -11.619 41.645 -13.117 1.00 4.06
+ATOM 82 CB ARG 42 -11.330 40.378 -13.313 1.00 5.19
+TER
+CONECT 1 3 2
+CONECT 3 5 4
+.
+.
+.
+CONECT 76 78 77
+CONECT 78 79
+CONECT 79 80
+CONECT 81 82
+TER
+REMARK 2HEP clustering 300K ENERGY -8.22572E+01 RMS 3.29
+ATOM 1 CA MET 1 -37.698 40.489 -32.408 1.00 5.96
+ATOM 2 CB MET 1 -38.477 39.426 -34.159 1.00 6.34
+.
+.
+.
+ATOM 80 CB PHE 41 -35.345 50.342 -31.371 1.00 2.62
+ATOM 81 CA ARG 42 -33.603 54.332 -27.130 1.00 4.06
+ATOM 82 CB ARG 42 -33.832 53.074 -24.415 1.00 5.19
+TER
+CONECT 1 3 2
+CONECT 3 5 4
+.
+.
+.
+CONECT 76 78 77
+CONECT 78 79
+CONECT 79 80
+CONECT 81 82
+TER
+\end{verbatim}
+
+\subsection{The conformation-distance file}
+\label{sect:inoutfiles:confdist}
+
+The file name is INPUT\_clust.rms. It contains the upper-diagonal part of
+the matrix of rmsds between conformations and differences between their
+energies:
+
+i,j,rmsd,energy(j)-energy(i) (format 2i5,2f10.5)
+
+where i and j, j$>$i are the numbers of the conformations, rmsd is the rmsd
+between conformation i and conformation j and energy(i) and energy(j) are
+the UNRES energies of conformations i and j, respectively.
+
+\subsection{The clustering-tree PicTeX file}
+\label{sect:inoutfiles:tree}
+
+This file contains the PicTeX code of the clustering tree. The file name is
+INPUT\_clust.tex. It should be supplemented with LaTeX preamble and final
+commands or incorporated into a LaTeX source and compiled with LaTeX. The
+picture is produced by running LaTeX followed by dvips, dvipdf or other command
+to convert LaTeX-generated dvi files into a human-readable files.
+
+\newpage
+
+\section{SUPPORT}
+\label{sect:support}
+
+ Dr. Adam Liwo\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
+ phone: +48 58 523 5430\\
+ fax: +48 58 523 5472\\
+ e-mail: \href{mailto:adam@chem.univ.gda.pl}{\textcolor{blue}{adam@chem.univ.gda.pl}}\\
+
+
+
+ Dr. Cezary Czaplewski\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
+ phone: +48 58 523 5430\\
+ fax: +48 58 523 5472\\
+ e-mail: \href{mailto:czarek@chem.univ.gda.pl}{czarek@chem.univ.gda.pl}
+
+
+Prepared by Adam Liwo, 02/19/12
+
+\LaTeX versioin, 09/28/12
+\end{document}
--- /dev/null
+\documentclass[12pt]{article}
+%\usepackage{latex2html}
+\usepackage{enumerate}
+\usepackage{longtable}
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{color}
+\parindent=0pt
+\parskip=12pt
+\textheight=24cm
+\textwidth=18cm
+\topmargin=-2.5cm
+\oddsidemargin=-0.5cm
+\setcounter{secnumdepth}{5}
+\setcounter{tocdepth}{5}
+\begin{document}
+\sloppy
+
+\title{XDRF2PDB, XDRF2PDB-M, XDRF2X\\
+Programs to convert compressed Cartesian coordinate files from UNRES into ASCII formats}
+
+\author{Department of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Sobieskiego 18\\ 80-952 Gdansk, Poland\\
+\\
+\\
+Scheraga Group\\ Baker Laboratory of Chemistry \\
+and Chemical Biology\\ Cornell University\\ Ithaca, NY 14853-1303, USA}
+
+\maketitle
+
+%
+%TABLE OF CONTENTS
+%
+%1. License terms
+%2. Programs and their functions
+%3. Installation
+%4. Command lines and files
+% 4.1 xdrf2pdb
+% 4.2 xdrf2pdb-m
+% 4.3 xdrf2x
+% 4.4 xdrf2ang
+%5. Support
+%
+\newpage
+
+\section{LICENSE TERMS}
+\label{sect:license}
+
+\begin{itemize}
+
+\item
+ This software is provided free of charge to academic users, subject to the condition that no part of it be sold or used otherwise for commercial purposes, including, but not limited to its incorporation into commercial software packages, without written consent from the authors. For permission contact Prof. H. A. Scheraga, Cornell University.
+
+\item
+ This software package is provided on an ``as is'' basis. We in no way warrant either this software or results it may produce.
+
+\item
+ Reports or publications using this software package must contain an acknowledgment to the authors and the NIH Resource in the form commonly used in academic research.
+
+\end{itemize}
+
+\newpage
+
+\section{PROGRAMS AND THEIR FUNCTONS}
+\label{sect:programs}
+
+The following three programs can be used to extract conformations from compressed Cartesian (cx) files from UNRES:
+
+\begin{description}
+
+\item{xdrf2pdb} --- takes a single trajectory file and converts it into PDB format.
+
+\item{xdrf2pdb-m} -- takes a multiple-trajectory file from UNRES/MREMD simulations and enables the user to extract conformation of a particular trajectory and save them to a PDB file.
+
+\item{xdrf2x} -- takes a single trajectory file and converts it into UNRES Cartesian coordinate (x) format.
+
+\item{xdrf2ang} -- takes a single trajectory file and calculates UNRES backbone angles (theta and gamma).
+
+\end{description}
+
+\section{INSTALLATION}
+\label{sect:install}
+
+Run make all on your system to install all programs or make {\it program} to install a particular program. You might need to run make in the xdrf subdirectory beforehand or point to the xdrf library that is on another directory in the Makefile.
+
+The programs compile on all known Fortran compilers, including gfortran.
+
+\section{COMMAND LINE AND FILES}
+\label{sect:command}
+
+For xdrf2pdb and xdrf2pdb-m, you'll need to prepare the UNRES sequence file in either one- or three-letter code.
+
+\subsection{XDRF2PDB}
+\label{sect:command:xdrf2pdb}
+
+Command line syntax:
+
+xdrf2pdb one/three seqfile cxfile [freq] [start] [end] [pdbfile]
+
+\begin{description}
+
+\item{one or three} indicates in what format the sequence will be read
+\item{seqfile} -- the file with the sequence:
+\begin{itemize}
+\item one-letter format: 80A1
+\item three-letter format: 20(A3,1X)
+\end{itemize}
+Note that the sequence must match exactly the UNRES sequence.
+\item{cxfile} -- full name of the trajectory file with compressed Cartesian coordinates.
+\item{freq} (1) -- conformation sampling frequency (each freq-th conformation will be saved to PBD file.
+\item{start} (1) -- the first conformation to be saved to PDB file.
+\item{end} (1000000000) -- the last conformation to be saved to PDB file.
+\item{pdbfile} (cxfile with extension changed from cx to pdb) -- the output PDB file.
+
+\end{description}
+
+\subsection{XDRF2PDB-M}
+\label{sect:command:xdrf2pdb-m}
+
+Command line syntax:
+
+xdrf2pdb-m one/three seqfile cxfile [ntraj] [itraj] [pdbfile] [ifreq]
+
+\begin{description}
+
+\item{cxfile} - the name of the compressed trajectory file from an UNRES/MREMD run carried out with TRAJ1FILE (conformations from all trajectories output to a single file).
+\item{ntraj} (1) -- number of trajectories in the multi-trajectory run.
+\item{itraj} (1) -- the number of trajectory to be extracted.
+
+\end{description}
+
+\subsection{XDRF2X}
+\label{sect:command:xdrf2x}
+
+Command line syntax:
+
+xdrf2x cxfile [is] [ie] [freq] $>$ x\_file
+
+The meaning of the the arguments is as in section
+\ref{sect:command:xdrf2pdb}; the conformations are output in UNRES Cartesian coordinate format to stdout.
+
+\subsection{XDRF2ANG}
+\label{sect:command:xdrf2ang}
+
+Command line syntax:
+
+xdrf2ang one/three seqfile cxfile [freq] [start] [end] [angfile]
+
+The meaning of the first six parameters is as in section \ref{sect:command:xdrf2pdb} angfile is
+ the name of the output angle file; is assigned cx file name with the cx
+ extension changed to ang, if not present.
+
+\section{SUPPORT}
+\label{sect:support}
+
+ Dr. Adam Liwo\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
+ phone: +48 58 523 5430\\
+ fax: +48 58 523 5472\\
+ e-mail: \href{mailto:adam@chem.univ.gda.pl}{\textcolor{blue}{adam@chem.univ.gda.pl}}\\
+
+
+
+ Dr. Cezary Czaplewski\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
+ phone: +48 58 523 5430\\
+ fax: +48 58 523 5472\\
+ e-mail: \href{mailto:czarek@chem.univ.gda.pl}{czarek@chem.univ.gda.pl}
+
+Prepared by Adam Liwo, 11/26/11
+
+\LaTeX version, 09/28/12
+
+\end{document}
--- /dev/null
+\documentclass[12pt]{article}
+%\usepackage{latex2html}
+\usepackage{enumerate}
+\usepackage{longtable}
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{color}
+\parindent=0pt
+\parskip=12pt
+\textheight=24cm
+\textwidth=18cm
+\topmargin=-2.5cm
+\oddsidemargin=-0.5cm
+\setcounter{secnumdepth}{5}
+\setcounter{tocdepth}{5}
+\begin{document}
+\sloppy
+
+\title{UNRES - A PROGRAM FOR COARSE-GRAINED SIMULATIONS OF PROTEINS}
+
+\author{Department of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Sobieskiego 18\\ 80-952 Gdansk, Poland\\
+\\
+\\
+Scheraga Group\\ Baker Laboratory of Chemistry \\
+and Chemical Biology\\ Cornell University\\ Ithaca, NY 14853-1303, USA}
+
+\maketitle
+
+\newpage
+
+\tableofcontents
+
+%TABLE OF CONTENTS
+%
+%1. License terms
+%2. Credits
+%3. General information
+% 3.1. Purpose
+% 3.2. Functions of the program
+% 3.3. Companion programs
+% 3.4. Programming language
+% 3.5. References
+%4. Installation
+%5. Customizing your batch and C-shell script
+%6. Command line and files
+%7. Force fields
+%8. Input files
+% 8.1. Main input data file
+% 8.1.1 Title
+% 8.1.2. Control data (data list format; READ_CONTROL subroutine)
+% 8.1.2.1 Keywords to chose calculation type
+% 8.1.2.2 Specification of protein and structure output in non-MD applications
+% 8.1.2.3. Miscellaneous
+% 8.1.3. Minimizer options (data list, subroutine READ_MINIM)
+% 8.1.4. CSA control parameters
+% 8.1.5. MCM data (data list, subroutine MCMREAD)
+% 8.1.6. MD data (subroutine READ_MDPAR)
+% 8.1.7. REMD/MREMD data (subroutine READ_REMDPAR)
+% 8.1.8. Energy-term weights (data list; subroutine MOLREAD)
+% 8.1.9. Input and/or reference PDB file name (text format; subroutine MOLREAD)
+% 8.1.10. Amino-acid sequence (free and text format)
+% 8.1.11. Disulfide-bridge information (free format; subroutine READ_BRIDGE)
+% 8.1.12. Dihedral-angle restraint data (free format; subroutine MOLREAD)
+% 8.1.13. Distance restraints (subroutine READ_DIST_CONSTR)
+% 8.1.14. Internal coordinates of the reference structure (free format; subroutine READ_ANGLES)
+% 8.1.15. Internal coordinates of the initial conformation (free format; subroutine READ_ANGLES)
+% 8.1.15.1. File name with internal coordinates of the conformations to be processed
+% 8.1.16 Control data for energy map construction (data lists; subroutine MAP_READ)
+% 8.2. Input coordinate files
+% 8.3. Other input files
+%9. Output files
+% 9.1. Coordinate files
+% 9.1.1. The internal coordinate (INT) files
+% 9.1.2. The plain Cartesian coordinate (X) files
+% 9.1.3. The compressed Cartesian coordinate (CX) files
+% 9.1.4. The Brookhaven Protein Data Bank format (PDB) files
+% 9.1.5. The SYBYLL (MOL2) files
+% 9.2. The summary (STAT) file
+% 9.2.1. Non-MD runs
+% 9.2.2. MD and MREMD runs
+% 9.3. CSA-specific output files
+%10. Technical support contact information
+%
+
+\newpage
+
+\section{LICENSE TERMS}
+\label{sect:license}
+
+\begin{itemize}
+
+\item
+ This software is provided free of charge to academic users, subject to the condition that no part of it be sold or used otherwise for commercial purposes, including, but not limited to its incorporation into commercial software packages, without written consent from the authors. For permission contact Prof. H. A. Scheraga, Cornell University.
+
+\item
+ This software package is provided on an ``as is'' basis. We in no way warrant either this software or results it may produce.
+
+\item
+ Reports or publications using this software package must contain an acknowledgment to the authors and the NIH Resource in the form commonly used in academic research.
+
+\end{itemize}
+
+\newpage
+
+\section{CREDITS}
+\label{sect:credits}
+
+The current and former developers of UNRES are listed in this section in alphabetic
+order together with their current or former affiliations.
+
+{\obeylines
+Maurizio Chinchio (formerly Cornell Univ., USA)
+Cezary Czaplewski (Univ. of Gdansk, Poland)
+Carlo Guardiani (Georgia State Univ., USA)
+Yi He (Cornell Univ., USA)
+Justyna Iwaszkiewicz (Swiss Institute of Bioinformatics, Switzerland)
+Dawid Jagiela (Univ. of Gdansk, Poland)
+Stanislaw Jaworski (deceased)
+Sebastian Kalinowski (Univ. of Gdansk, Poland)
+Urszula Kozlowska (deceased)
+Rajmund Kazmierkiewicz (Univ. of Gdansk, Poland)
+Jooyoung Lee (Korea Institute for Advanced Studies, Korea)
+Adam Liwo (Univ. of Gdansk, Poland)
+Mariusz Makowski (Univ. of Gdansk, Poland)
+Marian Nanias (formerly Cornell Univ., USA)
+Stanislaw Oldziej (Univ. of Gdansk, Poland)
+Jaroslaw Pillardy (Cornell Univ., USA)
+Daniel Ripoll (formerly Cornell Univ., USA)
+Jeff Saunders (Schrodinger Inc., USA)
+Harold A. Scheraga (Cornell Univ., USA)
+Hujun Shen (Dalian Institute of Chemical Physics, P.R. China)
+Adam Sieradzan (Univ. of Gdansk, Poland)
+Ryszard Wawak (formerly Cornell Univ., USA)
+Bartlomiej Zaborowski (Univ. of Gdansk, Poland)
+}
+
+\newpage
+
+\section{GENERAL INFORMATION}
+\label{sect:geninfo}
+
+\subsection{Purpose}
+\label{sect:geninfo:purpose}
+
+Run coarse-grained calculations of polypeptide chains with the UNRES force field.
+There are two versions of the package which should be kept separate because of
+non-overlapping functions: version which runs global optimization (Conformational
+Space Annealing, CSA) and version that runs coarse-grained molecular dynamics and
+its extension. Because the installation, input file preparation and running CSA
+and MD versions are similar, a common manual is provided. Items specific
+for the CSA and MD version are marked ``CSA'' and ``MD'', respectively.
+
+MD version can be used to run multiple-chain proteins (however, that version of
+the code is a new release and might fail if yet un-checked functions are used).
+The multi-chain CSA version for this purpose is another package (written largely in
+C++).
+
+\subsection{Functions of the program}
+\label{sect:geninfo:functions}
+
+\begin{enumerate}
+
+\item
+ Perform energy evaluation of a single or multiple conformations (serial and parallel) (CSA and MD).
+
+\item
+ Run canonical mesoscopic molecular dynamics (serial and parallel) (MD).
+
+\item
+ Run replica exchange (REMD) and multiplexing replica exchange (MREMD) dynamics (parallel only) (MD).
+
+\item
+ Run multicanonical molecular dynamics (parallel only) (MD).
+
+\item
+ Run energy minimization (serial and parallel) (CSA and MD).
+
+\item
+ Run conformational space annealing (CSA search) (parallel only) (CSA).
+
+\item
+ Run Monte Carlo plus Minimization (MCM) (parallel only) (CSA).
+
+\item
+ Run conformational family Monte Carlo (CFMC) calculations (CSA).
+
+\item
+ Thread the sequence against a database from the PDB and minimize energy of each structure (CSA).
+
+\end{enumerate}
+
+Energy and force evaluation is parallelized in MD version.
+
+
+\subsection{Companion programs}
+\label{sect:geninfo:companion}
+
+The structures produced by UNRES can be used as inputs to the following programs provided
+with this package or separately:
+
+\begin{description}
+
+\item{xdrf2pdb} -- converts the compressed coordinate files from MD (but not MREMD)runs into
+ PDB format.
+
+\item{xdrf2pdb-m} -- same for MREMD runs (multiple trajectory capacity).
+
+\item{xdrf2x} -- converts the plain Cartesian coordinate files into PDB format.
+
+\item{WHAM} -- processes the coordinate files from MREMD runs and computes temperature profiles
+ of ensemble averages and computes the probabilities of conformations at selected
+ temperatures; also prepares data for CLUSTER and ZSCORE.
+
+\item{CLUSTER} -- does the cluster analysis of the conformations; for MREMD runs takes the
+ coordinate files from WHAM which contain information to compute probabilities
+ of conformations at any temperature.
+
+\item{PHOENIX} -- conversion of UNRES conformations to all-atom conformations.
+
+\item{ZSCORE} -- force field optimization (for developers).
+
+\end{description}
+
+Please consult the manuals of the corresponding packages for details. Note that not
+all of these packages are released yet; they will be released depending on their
+readiness for distribution. Contact Adam Liwo, Cezary Czaplewski or Stanislaw Oldziej
+for developmental versions of these programs.
+
+\subsection{Programming language}
+\label{sect:geninfo:language}
+
+This version of UNRES is written almost exclusively in Fortran 77; some subroutines
+for data management are in ansi-C. The package was parallelized with MPI.
+
+\newpage
+
+\subsection{References}
+\label{sect:geninfo:references}
+
+Citing the following references in your work that makes use of UNRES is gratefully
+acknowledged:
+
+\begingroup
+\renewcommand{\section}[2]{}%
+\begin{thebibliography}{10}
+
+\bibitem{liwo_1997}
+ A. Liwo, S. Oldziej, M.R. Pincus, R.J. Wawak, S. Rackovsky, H.A. Scheraga.
+ A united-residue force field for off-lattice protein-structure simulations.
+ I: Functional forms and parameters of long-range side-chain interaction potentials
+ from protein crystal data. {\it J. Comput. Chem.}, {\bf 1997}, 18, 849-873.
+
+\bibitem{liwo_1997_02}
+ A. Liwo, M.R. Pincus, R.J. Wawak, S. Rackovsky, S. Oldziej, H.A. Scheraga.
+ A united-residue force field for off-lattice protein-structure simulations.
+ II: Parameterization of local interactions and determination
+ of the weights of energy terms by Z-score optimization.
+ {\it J. Comput. Chem.}, {\bf 1997}, 18, 874-887.
+
+\bibitem{liwo_1997_03}
+A. Liwo, S. O{\l}dziej, R. Ka\'zmierkiewicz, M. Groth, C. Czaplewski.
+Design of a knowledge-based force field for off-lattice simulations of protein
+structure.
+{\it Acta Biochim. Pol.}, {\bf 1997}, 44, 527-548.
+
+
+\bibitem{liwo_1998}
+ A. Liwo, R. Kazmierkiewicz, C. Czaplewski, M. Groth, S. Oldziej, R.J. Wawak,
+ S. Rackovsky, M.R. Pincus, H.A. Scheraga.
+ United-residue force field for off-lattice protein-structure simulations.
+ III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials.
+ {\it J. Comput. Chem.}, {\bf 1998}, 19, 259-276.
+
+\bibitem{liwo_2001}
+ A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Cumulant-based expressions for the multibody terms for the correlation between
+ local and electrostatic interactions in the united-residue force field.
+ {\it J. Chem. Phys.}, {\bf 2001}, 115, 2323-2347.
+
+\bibitem{lee_2001}
+ J. Lee, D.R. Ripoll, C. Czaplewski, J. Pillardy, W.J. Wedemeyer, H.A. Scheraga,
+ Optimization of parameters in macromolecular potential energy functions by
+ conformational space annealing. {\it J. Phys. Chem. B}, {\bf 2001}, 105, 7291-7298
+
+\bibitem{pillardy_2001}
+ J. Pillardy, C. Czaplewski, A. Liwo, W.J. Wedemeyer, J. Lee, D.R. Ripoll,
+ P. Arlukowicz, S. Oldziej, Y.A. Arnautova, H.A. Scheraga,
+ Development of physics-based energy functions that predict medium-resolution
+ structures for proteins of the $\alpha, \beta$, and $\alpha/\beta$ structural classes.
+ {\it J. Phys. Chem. B}, {\bf 2001}, 105, 7299-7311
+
+\bibitem{liwo_2002}
+ A. Liwo, P. Arlukowicz, C. Czaplewski, S. Oldziej, J. Pillardy, H.A. Scheraga.
+ A method for optimizing potential-energy functions by a hierarchical design
+ of the potential-energy landscape: Application to the UNRES force field.
+ {\it Proc. Natl. Acad. Sci. U.S.A.}, {\bf 2002}, 99, 1937-1942.
+
+\bibitem{saunders_2003}
+ J. A. Saunders and H.A. Scheraga.
+ Ab initio structure prediction of two $\alpha$-helical oligomers
+ with a multiple-chain united-residue force field and global search.
+ {\it Biopolymers}, {\bf 2003}, 68, 300-317.
+
+\bibitem{saunders_2003_02}
+ J.A. Saunders and H.A. Scheraga.
+ Challenges in structure prediction of oligomeric proteins at the united-residue
+ level: searching the multiple-chain energy landscape with CSA and CFMC procedures.
+ {\it Biopolymers}, {\bf 2003}, 68, 318-332.
+
+\bibitem{oldziej_2003}
+ S. Oldziej, U. Kozlowska, A. Liwo, H.A. Scheraga.
+ Determination of the potentials of mean force for rotation about C$^\alpha$-C$^\alpha$
+ virtual bonds in polypeptides from the ab initio energy surfaces of terminally
+ blocked glycine, alanine, and proline. {\it J. Phys. Chem. A}, {\bf 2003}, 107, 8035-8046.
+
+\bibitem{liwo_2004}
+ A. Liwo, S. Oldziej, C. Czaplewski, U. Kozlowska, H.A. Scheraga.
+ Parameterization of backbone-electrostatic and multibody contributions
+ to the UNRES force field for protein-structure prediction from ab initio
+ energy surfaces of model systems. {\it J. Phys. A}, {\bf 2004}, 108, 9421-9438.
+
+\bibitem{oldziej_2004}
+ S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 2. Off-lattice tests of the method with single
+ proteins. {\it J. Phys. Chem. B.}, {\bf 2004}, 108, 16934-16949.
+
+\bibitem{oldziej_2004_02}
+ S. Oldziej, J. Lagiewka, A. Liwo, C. Czaplewski, M. Chinchio,
+ M. Nanias, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 3. Use of many proteins in optimization.
+ {\it J. Phys. Chem. B.}, {\bf 2004}, 108, 16950-16959.
+
+\bibitem{oldziej_2004_03}
+ M. Khalili, A. Liwo, F. Rakowski, P. Grochowski, H.A. Scheraga.
+ Molecular dynamics with the united-residue model of polypeptide chains.
+ I. Lagrange equations of motion and tests of numerical stability in the
+ microcanonical mode, {\it J. Phys. Chem. B}, {\bf 2005}, 109, 13785-13797.
+
+\bibitem{khalili_2005}
+ M. Khalili, A. Liwo, A. Jagielska, H.A. Scheraga.
+ Molecular dynamics with the united-residue model of polypeptide chains.
+ II. Langevin and Berendsen-bath dynamics and tests on model $\alpha$-helical
+ systems. {\it J. Phys. Chem. B}, {\bf 2005}, 109, 13798-13810.
+
+\bibitem{khalili_2005_02}
+ A. Liwo, M. Khalili, H.A. Scheraga.
+ Ab initio simulations of protein-folding pathways by molecular dynamics with
+ the united-residue model of polypeptide chains.
+ {\it Proc. Natl. Acad. Sci. U.S.A.}, {\bf 2005}, 102, 2362-2367.
+
+\bibitem{rakowski_2006}
+ F. Rakowski, P. Grochowski, B. Lesyng, A. Liwo, H. A. Scheraga.
+ Implementation of a symplectic multiple-time-step molecular dynamics algorithm,
+ based on the united-residue mesoscopic potential energy function.
+ {\it J. Chem. Phys.}, {\bf 2006}, 125, 204107.
+
+\bibitem{nanias_2006}
+ M. Nanias, C. Czaplewski, H.A. Scheraga.
+ Replica exchange and multicanonical algorithms with the coarse-grained
+ united-residue (UNRES) force field.
+ {\it J. Chem. Theory and Comput.}, {\bf 2006}, 2, 513-528.
+
+\bibitem{liwo_2007}
+ A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, K. Wachucik, H.A. Scheraga.
+ Modification and optimization of the united-residue (UNRES) potential energy
+ function for canonical simulations. I. Temperature dependence of the effective
+ energy function and tests of the optimization method with single training
+ proteins.
+ {\it J. Phys. Chem. B}, {\bf 2007}, 111, 260-285.
+
+\bibitem{kozlowska_2007}
+ U. Kozlowska, A. Liwo, H.A. Scheraga.
+ Determination of virtual-bond-angle potentials of mean force for coarse-grained
+ simulations of protein structure and folding from ab initio energy surfaces of
+ terminally-blocked glycine, alanine, and proline.
+ {\it J. Phys.: Condens. Matter}, {\bf 2007}, 19, 285203.
+
+\bibitem{chichio_2007}
+ M. Chinchio, C. Czaplewski, A. Liwo, S. Oldziej, H.A. Scheraga.
+ Dynamic formation and breaking of disulfide bonds in molecular dynamics
+ simulations with the UNRES force field.
+ {\it J. Chem. Theory Comput.}, {\bf 2007}, 3, 1236-1248.
+
+\bibitem{rojas_2007}
+ A.V. Rojas, A. Liwo, H.A. Scheraga.
+ Molecular dynamics with the united-residue force field: Ab Initio folding
+ simulations of multichain proteins.
+ {\it J. Phys. Chem. B}, {\bf 2007}, 111, 293-309.
+
+\bibitem{liwo_2008}
+ A. Liwo, C. Czaplewski, S. Oldziej, A.V. Rojas, R. Kazmierkiewicz,
+ M. Makowski, R.K. Murarka, H.A. Scheraga.
+ Simulation of protein structure and dynamics with the coarse-grained UNRES
+ force field. In: Coarse-Graining of Condensed Phase and Biomolecular
+ Systems., ed. G. Voth, Taylor \& Francis, 2008, Chapter 8, pp. 107-122.
+
+\bibitem{czaplewski_2009}
+ C. Czaplewski, S. Kalinowski, A. Liwo, H.A. Scheraga.
+ Application of multiplexed replica exchange molecular dynamics
+ to the UNRES force field: tests with $\alpha$ and $\alpha+\beta$ proteins.
+ {\it J. Chem. Theory Comput.}, {\bf 2009}, 5, 627-640.
+
+\bibitem{he_2009}
+ Y. He, Y. Xiao, A. Liwo, H.A. Scheraga.
+ Exploring the parameter space of the coarse-grained UNRES force field by random
+ search: selecting a transferable medium-resolution force field.
+ {\it J. Comput. Chem.}, {\bf 2009}, 30, 2127-2135.
+
+\bibitem{kozlowska_2010}
+ U. Kozlowska, A. Liwo. H.A. Scheraga.
+ Determination of side-chain-rotamer and side-chain and backbone
+ virtual-bond-stretching potentials of mean force from AM1 energy surfaces of
+ terminally-blocked amino-acid residues, for coarse-grained simulations of
+ protein structure and folding. 1. The Method.
+ {\it J. Comput. Chem.}, {\bf 2010}, 31, 1143-1153.
+
+\bibitem{kozlowska_2010_02}
+ U. Kozlowska, G.G. Maisuradze, A. Liwo, H.A. Scheraga.
+ Determination of side-chain-rotamer and side-chain and backbone
+ virtual-bond-stretching potentials of mean force from AM1 energy surfaces of
+ terminally-blocked amino-acid residues, for coarse-grained simulations of
+ protein structure and folding. 2. Results, comparison with statistical
+ potentials, and implementation in the UNRES force field.
+ {\it J. Comput. Chem.}, {\bf 2010}, 31, 1154-1167.
+
+\bibitem{liwo_2010}
+ A. Liwo, S. Oldziej, C. Czaplewski, D.S. Kleinerman, P. Blood, H.A. Scheraga.
+ Implementation of molecular dynamics and its extensions with the coarse-grained
+ UNRES force field on massively parallel systems; towards millisecond-scale
+ simulations of protein structure, dynamics, and thermodynamics.
+ {\it J. Chem. Theory Comput.}, {\bf 2010}, 6, 890-909.
+
+\end{thebibliography}
+\endgroup
+
+\newpage
+
+\section{INSTALLATION}
+\label{sect:install}
+
+The distribution is contained in the UNRES.tar.gz file. To uncompress say:
+
+\begin{verbatim}
+gzip -cd UNRES.tar.gz | tar xf -
+\end{verbatim}
+
+This will produce a directory named UNRES with the following subdirectories:
+
+\begin{description}
+
+\item{src\_CSA} -- the CSA-version source directory.
+
+\item{src\_MD} -- the MD-version source directory, single chains.
+
+\item{src\_MD-M} -- the MD-version source directory, oligomeric proteins
+
+\item{bin} -- the binaries/scripts directory; its BATCH\_SCRIPTS directory contains the
+ batch scripts (at present the only example is for PBS: unres\_3P\_PBS.csh,
+ which is an UNRES calling script and start.mat, which is the batch script
+ submitted to the PBS system).
+
+\item{doc} -- documentation (this file and EXAMPLES.TXT)
+
+\item{examples} -- sample input files (see EXAMPLES.TXT for description).
+
+\end{description}
+
+To produce the executable do the following:
+
+\begin{enumerate}[(a)]
+%a)
+\item
+ To build parallel version, make sure that MPI is installed in your system.
+ Note that the package will have limited functions when compiled in a single-CPU mode.
+ On linux cluster the command source \$HOME/.env should be added to .tcshrc
+ or equivalent file to use parallel version of the program, the
+ alternative is to use queuing system like PBS.
+ In some cases the FORTRAN library subroutine GETENV does not work properly
+ with MPI, if the script is run interactively. In such a case try to
+ add the source mygentenv.F and turn on the -DMYGETENV preprocessor flag.
+%b)
+\item
+ Change directory to the respective source directory.
+%c)
+\item
+ Edit the appropriate Makefile (parallel program that includes CSA
+ procedure, the serial version is no longer supported, for serial task
+ parallel program can be run using only one processor) to customize to your
+ system. Makefiles for the following systems are provided:
+
+ Makefile\_osf\_f90 - OSF1/Tru64 UNIX HP Alphaserver with f90 compiler,
+ Makefile\_lnx\_pgf90 - Linux, the pgf90 compiler,
+ Makefile\_lnx\_ifc - Linux, ifc compiler.
+ Makefile\_win\_pgf90 - Windows, the pgf90 compiler.
+
+ Other systems should not cause problems; all you have to do is to change
+ the compiler, compiler options, and preprocessor options. Also, change the
+ BIN variable, if you want to put your binaries in other place than
+ PROTARCH/BIN. In the case of Makefile make sure that the MPI directories are
+ correctly specified.
+
+ The following architectures are defined in the .F source files:
+
+\begin{description}
+
+ \item{AIX} -- AIX systems (put -DAIX as one of the preprocessor options, if
+ this is your system).
+
+ \item{LINUX} -- Linux (put -DLINUX).
+
+ \item{G77} -- Gnu-Fortran compilers (might require sum moderate source code editing)
+ (put -DG77). The recommended compiler is gfortran and not g77.
+
+ \item{PGI} -- PGI compilers.
+
+ \item{WINPGI} -- additional setting for PGI compilers for MS Windows.
+
+ \item{SGI} -- all SGI platforms; should also be good for SUN platforms (put -DSGI).
+
+ \item{WIN} -- MS Windows with Digital Fortran compiler (put -DWIN)
+
+\end{description}
+
+ For other platforms, the only problems might appear in connection with
+ machine-specific I/O instructions. Many files are opened in the append
+ mode, whose specification in the OPEN statement is quite machine-dependent.
+ In this case you might need to modify the source code accordingly.
+ The other platform dependent routines are the timing routines contained
+ in timing.F. In addition to the platforms specified above, ES9000, SUN,
+ KSR, and CRAY are defined there.
+
+ For parallel build -DMP and -DMPI must be set (these are set in Makefile).
+
+ IMPORTANT! Apart from this, two define flags: -DCRYST\_TOR and -DMOMENT
+ define earlier versions of the force field. The MUST NOT be entered, if
+ the CASP5 and later versions of the force field are used.
+
+%d)
+\item
+ Build the unres executables by typing at your UNIX prompt:
+
+\begin{verbatim}
+ make # will build unres
+ make clean # will remove the object files
+\end{verbatim}
+
+ The bin directory contains pre-built binaries for Red Hat Linux. These
+ executables are specified in the csh scripts listed in section 4.
+
+%e)
+\item
+ Customize the C-shell scripts unres.unres (to run the parallel version on
+ set of workstation). See the next section of this manual for guidance.
+
+After the executables are build and C-shell scripts customized, you can run the
+test examples contained in UNRES/examples.
+
+\end{enumerate}
+
+\newpage
+
+\section{CUSTOMIZING YOUR C-SHELL SCRIPT}
+\label{sect:custom}
+
+IMPORTANT NOTE -- The unres.csh script is for Linux and should also be easily
+adaptable to other systems running MPICH. This script is for interactive
+parallel jobs. Examples of scripts compatible with PBS (pbs.sub) and LoadLever
+(sp2.sub) queuing systems are also provided.
+
+Edit the following lines in your unres.csh script:
+
+\begin{verbatim}
+set DD = your_database_directory
+\end{verbatim}
+
+e.g., if you installed the package on the directory /usr/local, this line
+looks like this:
+
+\begin{verbatim}
+set DD = /usr/local/UNRES/PARAM
+set BIN = your_binaries_directory
+set FGPROCS = number_of_processors_per_energy/force_evaluation (MD)
+\end{verbatim}
+
+e.g., if the root directory is as above:
+
+\begin{verbatim}
+set BIN = /usr/local/UNRES/bin
+\end{verbatim}
+
+\section{COMMAND LINE AND FILES}
+\label{sect:command}
+
+To run UNRES interactively enter the following command at your Unix prompt
+or put it in the batch script:
+
+\begin{verbatim}
+unres.csh POTENTIAL INPUT N_PROCS
+\end{verbatim}
+
+where:
+
+POTENTIAL specifies the side-chain interaction potential type and must be
+one of the following:
+
+\begin{description}
+
+\item{LJ} -- 6-12 radial Lennard-Jones.
+
+\item{LJK} -- 6-12 radial Lennard-Jones-Kihara (shifted Lennard Jones).
+
+\item{BP} -- 6-12 anisotropic Berne-Pechukas based on Gaussian overlap (dilated
+ Lennard-Jones).
+
+\item{GB} -- 6-12 anisotropic Gay-Berne (shifted Lennard-Jones).
+
+\item{GBV} -- 6-12 anisotropic Gay-Berne-Vorobjev (shifted Lennard-Jones).
+
+See section \ref{sect:forcefields} (Force Fields) for explanation and usage.
+
+At present, only the LJ and GB potentials are applied. The LJ potential
+is used in the ``CASP3'' version of the UNRES force field that is able
+to predict only $\alpha$-helical structures. All further version of the
+UNRES force field use the GB potential. For the description of all above-mentioned
+potentials see ref. \cite{liwo_1997_02}.
+
+\item{INPUT} is the prefix for input and output files (see below)
+
+\item{N\_PROCS} is the number of processors; for a CSA or REMD/MREMD run it MUST be at least 2.
+
+\end{description}
+
+Note! The script takes one more variable, FGPROCS, as the fourth argument,
+which is the number of fine-grain processors to parallelize energy
+evaluations. The corresponding code is in UNRES/CSA, but it was written
+using MPL instead of MPI and therefore is never used in the present version.
+At present we have no plans to rewrite fine-grain parallelization using MPI,
+because we found that the scalability for up to 200 residue polypeptide
+chains was very poor, due to a small number of interactions and,
+correspondingly, unfavorable ratio of the overhead to the computation time.
+
+\begin{description}
+
+\item{INPUT.inp} contains the main input data and the control parameters of the CSA
+ method.
+
+\item{INPUT.out\_POTENTIAL\_xxx} is the main output files from different processors; xxx
+ denotes the number of the processor
+
+\item{INPUT\_POTENTIALxxx.stat} is the summary files with the energies, energy components,
+ and RMS deviations of the conformations produced by each of the processors;
+ not used in CSA runs; also it outputs different quantity in MD/MREMD runs.
+
+CSA version specific files:
+
+\item{INPUT\_POTENTIALxxx.int} is the internal coordinates; in the CSA run
+
+\item{INPUT\_POTENTIAL\_000.int} contains the coordinates of the conformations,
+ and the other files are empty
+
+\item{INPUT.CSA.history} is the history file from a CSA run. This is an I/O file, because
+ it can be used to restart an interrupted CSA run.
+
+\item{INPUT.CSA.seed} stores the random seed generated in a CSA run; written for
+ restart purposes.
+
+\item{INPUT.CSA.bank} is the current bank of conformations obtained in CSA calculations
+ (expressed as internal coordinates). This information is also stored in
+ INPUT\_POTENTIAL000.int
+
+\item{INPUT.CSA.rbank} -- as above, but contains random-generated conformations.
+
+\end{description}
+
+MD version specific files:
+
+\begin{description}
+
+\item{INPUT\_MDyyy.pdb} is the Cartesian coordinates of the conformations in PDB format.
+
+\item{INPUT\_MDyyy.x} is the Cartesian coordinates of the conformations in ASCII format.
+
+\item{INPUT\_MDyyy.cx} is the Cartesian coordinates of the conformations in compressed format
+ (need xdr2pdb to convert to PDB format).
+\end{description}
+
+The program currently produces some more files, but they are not used
+for any purposes and most of them are scratched after a run is completed.
+
+The run script also contains definitions of the parameter files through the
+following environmental variables:
+
+\begin{description}
+
+\item{SIDEPAR} -- parameters of the SC-SC interaction potentials ($U_{SC SC}$);
+
+\item{SCPPAR} -- parameters of the SC-p interaction potential ($U_{SCp}$); this file can
+ be ignored by specifying the -DOLDSCP preprocessor flag, which means that the
+ built-in parameters are used; at present they are the same as the parameters
+ in the file specified by SCPPAR;
+
+\item{ELEPAR} -- parameters of the p-p interaction potentials ($U_{pp}$);
+
+\item{FOURIER} -- parameters of the multibody potentials of the coupling between the
+ backbone-local and backbone-electrostatic interactions ($U_{corr}$);
+
+\item{THETPAR} -- parameters of the virtual-bond-angle bending potentials ($U_b$);
+
+\item{ROTPAR} -- parameters of the side-chain rotamer potentials ($U_{rot}$);
+
+\item{TORPAR} -- parameters of the torsional potentials ($U_{rot}$);
+
+\item{TORDPAR} -- parameters of the double-torsional potentials.
+
+\item{SCCORPAR} -- parameters of the supplementary torsional sequence-specific potentials.
+ (implemented recently).
+
+\end{description}
+
+\newpage
+
+\section{FORCE FIELDS}
+\label{sect:forcefields}
+
+UNRES is being developed since 1997 and several versions of the force field
+were produced. The settings and references to these force fields are
+summarized below.
+
+Force fields for CSA version (can be used in MD but haven't been parameterized for this
+purpose).
+
+{\small
+\hspace{-2cm}\begin{longtable}{|l|l|l|l|l|l|l|}\hline
+\small
+%---------------------------------------------------------------------------------------
+ & Additional & SC-SC & Example script & Structural &\\
+Force field & compiler flags& potential& and executables & classes covered& References\\
+ & & & (Linux; PGF90 &&\\
+ & & & and IFC) &&\\ \hline
+%---------------------------------------------------------------------------------------
+CASP3 & -DCRYST\_TOR & LJ & unres\_CASP3.csh &only $\alpha$ &\cite{liwo_1997,liwo_1997_02,liwo_1998}\\
+ & -DCRYST\_BOND & &unres\_pgf90\_cryst\_tor.exe&&\\
+ & -DCRYST\_THETA & &unres\_ifc6\_cryst\_tor.exe &&\\
+ & -DCRYST\_SC &&&&\\
+ & -DMOMENT &&&&\\
+&&&&&\\
+ALPHA & -DMOMENT & GB & unres\_CASP4.csh &only $\alpha$ &\cite{liwo_2001,lee_2001,pillardy_2001}\\
+ & -DCRYST\_BOND & &unres\_pgf90\_moment.exe &&\\
+ & -DCRYST\_THETA & &unres\_ifc6\_moment.exe &&\\
+ & -DCRYST\_SC &&&&\\
+&&&&&\\
+BETA & -DMOMENT & GB & unres\_CASP4.csh &only $\beta$ &\cite{liwo_2001,lee_2001,pillardy_2001}\\
+ & -DCRYST\_BOND & &unres\_pgf90\_moment.exe &&\\
+ & -DCRYST\_THETA & &unres\_ifc6\_moment.exe &&\\
+ & -DCRYST\_SC&&&&\\
+&&&&&\\
+ALPHABETA & -DMOMENT & GB & unres\_CASP4.csh & all &\cite{liwo_2001,lee_2001,pillardy_2001}\\
+ & -DCRYST\_BOND & &unres\_pgf90\_moment.exe &&\\
+ & -DCRYST\_THETA & &unres\_ifc6\_moment.exe &&\\
+ & -DCRYST\_SC &&&&\\
+&&&&&\\
+CASP5 & -DCRYST\_BOND & GB & unres\_CASP5.csh & all &\cite{liwo_2002,saunders_2003,saunders_2003_02,liwo_2004}\\
+ & -DCRYST\_THETA & & unres\_pgf90.exe &&\\
+ & -DCRYST\_SC & & unres\_ifc6.exe &&\\
+&&&&&\\
+3P & -DCRYST\_BOND & GB & unres\_3P.csh & all &\cite{oldziej_2004,oldziej_2004_02}\\
+ & -DCRYST\_THETA & & unres\_pgf90.exe &&\\
+ & -DCRYST\_SC & & unres\_ifc6.exe &&\\
+&&&&&\\
+4P & -DCRYST\_BOND & GB & unees\_4P.csh & all &\cite{oldziej_2004,oldziej_2004_02}\\
+ & -DCRYST\_THETA & & unres\_pgf90.exe&&\\
+ & -DCRYST\_SC & & unres\_ifc6.exe&&\\ \hline
+%---------------------------------------------------------------------------------------
+\end{longtable}
+}
+
+\newpage
+
+Force fields for MD version \cite{khalili_2005,khalili_2005_02}.
+
+{\small
+\begin{longtable}{|l|l|l|l|l|l|l|}\hline
+%---------------------------------------------------------------------------------------
+ & Additional & SC-SC & Example script & Structural &\\
+Force field & compiler flags& potential& and executables & classes covered& References\\
+ & & & (Linux; PGF90&&\\
+ & & & and IFC)&&\\ \hline
+%---------------------------------------------------------------------------------------
+GAB & -DCRYST\_BOND & GB & unres\_GAB.csh & mostly $\alpha$ & \cite{liwo_2007}\\
+ & -DCRYST\_THETA &&&&\\
+ & -DCRYST\_SC &&&&\\
+&&&&&\\
+E0G & -DCRYST\_BOND & GB & unres\_E0G.csh & mostly $\alpha$ & \cite{liwo_2007}\\
+ & -DCRYST\_THET &&&&\\
+ & -DCRYST\_SC &&&&\\
+&&&&&\\
+1L2Y\_1LE1 & none & GB & unres\_ab.csh & all & \cite{liwo_2007,kozlowska_2007,he_2009,kozlowska_2010,kozlowska_2010_02}\\ \hline
+%---------------------------------------------------------------------------------------
+\end{longtable}
+}
+
+The example scripts (the *.csh filed) contain all appropriate parameter files, while
+the energy-term weights are provided in the example input files listed in EXAMPLES.TXT
+(*.inp; see section \ref{sect:input}. for description of the input files). However, it is user's
+responsibility to specify appropriate compiler flags. Note that a version WILL NOT work,
+if the force-field specific compiler flags are not set. The parameter files specified
+in the run script also must strictly correspond to the energy-term weights specified in
+the input file. The parameter files for specific force fields are also specified below
+and the energy-term weights are specified in section \ref{sect:input}.
+
+The parameter files are as follows (the environment variables from section \ref{sect:command} are
+used to identify the parameters):
+
+CASP3:
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm \\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_cryst.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm (not used)\\
+SIDEPAR &scinter\_LJ.parm\\
+ELEPAR &electr.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_GAP.parm (not used)\\
+SCCORPAR&rotcorr\_AM1.parm (not used)\\
+\end{longtable}
+
+ALPHA, BETA, ALPHABETA (CASP4):
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm \\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_ecepp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm (not used)\\
+SIDEPAR &scinter\_GB.parm\\
+ELEPAR &electr.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_GAP.parm\\
+SCCORPAR&rotcorr\_AM1.parm (not used)\\
+\end{longtable}
+
+CASP5:
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm\\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_631Gdp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm\\
+SIDEPAR &scinter\_GB.parm\\
+ELEPAR &electr\_631Gdp.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_opt.parm.1igd\_iter7n\_c\\
+SCCORPAR&rotcorr\_AM1.parm (not used)\\
+\end{longtable}
+
+3P:
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm\\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_631Gdp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm\\
+SIDEPAR &sc\_GB\_opt.3P7\_iter81\_1r\\
+ELEPAR &electr\_631Gdp.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
+SCCORPAR&rotcorr\_AM1.parm (not used)\\
+\end{longtable}
+
+4P:
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm\\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_631Gdp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm\\
+SIDEPAR &sc\_GB\_opt.4P5\_iter33\_3r\\
+ELEPAR &electr\_631Gdp.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
+SCCORPAR&rotcorr\_AM1.parm (not used)\\
+\end{longtable}
+
+GAB:
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm\\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_631Gdp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm\\
+SIDEPAR &sc\_GB\_opt.1gab\_3S\_qclass5no310-shan2-sc-16-10-8k\\
+ELEPAR &electr\_631Gdp.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
+SCCORPAR&rotcorr\_AM1.parm\\
+\end{longtable}
+
+E0G:
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm\\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_631Gdp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm\\
+SIDEPAR &sc\_GB\_opt.1e0g-52-17k-2k-newclass-shan1e9\_gap8g-sc\\
+ELEPAR &electr\_631Gdp.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
+SCCORPAR&rotcorr\_AM1.parm\\
+\end{longtable}
+
+1L2Y\_1LE1:
+
+\begin{longtable}{ll}
+BONDPAR &bond\_AM1.parm\\
+THETPAR &theta\_abinitio.parm\\
+ROTPAR &rotamers\_AM1\_aura.10022007.parm\\
+TORPAR &torsion\_631Gdp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm\\
+SIDEPAR &scinter\_\${POT}.parm\\
+ELEPAR &electr\_631Gdp.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
+SCCORPAR&rotcorr\_AM1.parm\\
+\end{longtable}
+
+Additionally, for 1L2Y\_1LE1, the following environment variables and files are required
+to generate random conformations:
+
+THETPARPDB thetaml.5parm\\
+ROTPARPDB scgauss.parm
+
+For CSA, the best force field is 4P. For MD, the 1L2Y\_1LE1 force field is best for
+ab initio prediction but provides medium resolution (5 A for 60-residue proteins) and
+overemphasizes $\beta$-structures and has to be run with secondary-structure-prediction
+information. For prediction of the structure of mostly $\alpha$-protein, and for running
+dynamics of large proteins, the best is the GAB force field. All these force fields
+were trained by using our procedure of hierarchical optimization \cite{oldziej_2004,oldziej_2004_02}.
+The 4P and 1L2Y\_1LE1 force fields have considerable power independent of structural class.
+The ALPHA, BETA, and ALPHABETA force fields (for CSA) were used in the CASP4 exercises
+and the CASP5 force field was used in the CASP5 exercise with some success; ALPHA
+predicts reasonably the structure of $\alpha$-helical proteins and is still not obsolete,
+while for $\beta$- and $\alpha+\beta$-structure prediction
+3P or 4P should be used, because they are cheaper and more reliable than BETA and
+ALPHABETA. The early CASP3 force field is included for historical reasons only.
+
+\newpage
+
+\section{INPUT FILES}
+\label{sect:input}
+
+\subsection{Main input data file}
+\label{sect:input:main}
+
+Most of the data are organized as data lists, where the data can be put
+in any order, using a series of statements of the form:
+
+KEYWORD=value
+
+for simple non-logical variables
+
+or just
+
+KEYWORD
+
+to indicate that the corresponding option is turned on. For array variables
+the assignment statement is:
+
+KEYWORD=value1,value2,...
+
+However, the data lists are unnamed and that must be placed EXACTLY in the
+order indicated below. The presence of an \& in the 80th column of a line
+indicates that the next line will belong to the same data group. The parser
+subroutines that interpret the keywords are case insensitive.
+
+Each group of data organized as a data list is indicated as data list format
+input.
+
+\subsubsection{Title}
+\label{sect:input:main:title}
+
+Any string containing up to 80 characters. The first input line is always
+interpreted as title.
+
+\subsubsection{Control data}
+\label{sect:input:main:control}
+
+This data section is in data list format and is read in the READ\_CONTROL subroutine.
+
+\paragraph{Keywords to chose calculation type}
+
+\begin{description}
+
+\item{OUT1FILE} -- only the master processor prints the output file in a parallel job
+
+\item{MINIMIZE} -- if present, energy minimization will be carried out.
+
+\item{REGULAR} -- regularize the read in conformation (usually a crystal or
+ NMR structure) by doing a series of three constrained minimizations,
+ to keep the structure as close as possible to the starting
+ (experimental) structure. The constraints are the CA-CA distances
+ of the initial structure. The constraints are gradually diminished
+ and removed in the last minimization.
+
+\item{SOFTREG} -- regularize the read in conformation (usually a crystal or NMR
+ structure) by doing a series of constrained minimizations, with
+ additional use of soft potential and secondary structure
+ freezing, to keep the structure as close as possible to the
+ starting (experimental) structure.
+
+
+\item{CSA} -- if present, the run is a CSA run. At present, this is the only
+ reliable mode of doing global conformational search with this
+ package; it is NOT recommended to use MCM or THREAD for this
+ purpose.
+
+\item{MCM} -- if present, this is a Monte Carlo Minimization (MCM) run.
+
+\item{MULTCONF} -- if present, conformations will be read from the INPUT.intin
+ file.
+
+\item{MD} -- run canonical MD (single or multiple trajectories).
+
+\item{RE} -- run REMD or MREMD (parallel jobs only).
+
+\item{MUCA} -- run multicanonical MD calculations (parallel jobs only).
+
+\item{MAP=number} (integer) --
+Conformational map will be calculated in chosen angles.
+
+\item{THREAD=number} (integer) --
+Threading or threading-with-minimization run, using a database of structures
+contained in the \$DD/patterns.cart pattern data base (502 chains or chain
+fragments), using a total number patterns. It is recommended to use this with
+energy minimization; this implies regularization of each minimized pattern.
+See refs. \cite{liwo_1997_02} and \cite{liwo_1997_03}.
+
+\item{CHECKGRAD} -- compare numerical and analytical gradient; to be followed by:
+
+\item{CART} -- energy gradient in virtual-bond vectors (Cartesian coordinates)
+
+\item{INT} -- energy gradient in internal coordinates (default)
+
+\item{CARINT} -- derivatives of the internal coordinates in the virtual-bond vectors.
+
+\end{description}
+
+\paragraph{Specification of protein and structure output in non-MD applications}
+
+\begin{description}
+
+\item{ONE\_LETTER} -- one-letter and not three-letter code of the amino-acid residues
+ is used.
+
+\item{SYM} (1) -- number of chains with same sequence (for oligomeric proteins only).
+
+\item{PDBSTART} -- the initial conformation is read in from a PDB file.
+
+\item{UNRES\_PDB} -- the starting conformation is in UNRES representation (C$^\alpha$
+ and SC coordinates only). This keyword MUST appear in such a case
+ or the program will generate erroneous and unrealistic side-chain
+ coordinates.
+
+\item{RAND\_CONF} -- start from a random conformation.
+
+\item{EXTCONF} -- start from an extended chain conformation.
+
+\item{PDBOUT} -- if present, conformations will be output in PDB format. Note that
+ this keyword affects only the output from single energy evaluation,
+ energy minimization and multiple-conformation data. To request
+ conformations from MD/MREMD runs in PDB format, the MDPDB keyword
+ must be placed on the MD input record.
+
+\item{MOL2OUT} -- if present, conformations will be output in SYBYL mol2 format.
+
+\item{REFSTR} -- if present, reference structure will be read (e.g., to monitor
+ the RMS deviation from the crystal structure).
+
+\item{PDBREF} -- if present, a reference structure will be read in to compare
+ the calculated conformations with it.
+
+\item{UNRES\_PBD} -- the starting/reference structure is read from an UNRES-generated
+ PDB file.
+
+\end{description}
+
+Keywords: PDBOUT, MOL2OUT, PDBREF, and PDBSTART are ignored for a CSA run.
+Output mode for MD version is specified in MD input (see section \ref{sect:input:main:MD}).
+
+\paragraph{Miscellaneous}
+
+\begin{description}
+
+\item{CONSTR\_DIST=number}
+
+\begin{description}
+\item{0} -- no distance restraints,
+\item{$>0$} -- imposes harmonic restraints on selected distances; see section 5.12.
+In MD version, also restraints on the q variable \cite{liwo_2007} can be used.
+\end{description}
+
+\item{WEIDIS=number} (real)
+the weight of the distance term; applies for REGULARIZE and THREAD, otherwise
+ignored.
+
+\item{USE\_SEC\_PRED} -- use secondary-structure prediction information.
+
+\item{SEED=number} (integer) (no default)
+Random seed (required, even if the run is not a CSA, MCM, MD or MREMD run).
+
+\item{PHI} -- only the virtual-bond dihedral angles $\gamma$ are considered as
+ variables in energy minimization.
+
+\item{BACK} -- only the backbone virtual angles (virtual-bond angles theta and
+ virtual-bond dihedral angles $\gamma$) are considered as variables
+ in energy minimization.
+
+By default, all internal coordinates: $\theta$, $\gamma$, and the side-chain
+centroid polar angles $\alpha$ and $\beta$ are considered as variables in energy
+minimization.
+
+\item{RESCALE\_MODE=number} (real)
+Choice of the type of temperature dependence of the force field.
+\begin{description}
+\item{0} -- no temperature dependence
+\item{1} -- homographic dependence (not implemented yet with any force field)
+\item{2} -- hyperbolic tangent dependence \cite{liwo_2007}.
+\end{description}
+
+\item{T\_BATH=number} (real)
+temperature (for MD runs and temperature-dependent force fields).
+\end{description}
+
+The following keywords apply to MCM only:
+
+\begin{description}
+
+\item{MAXGEN=number} (integer) (10000)
+maximum number of conformations generated in a single MCM iteration
+
+\item{MAXOVERLAP=number} (integer) (1000)
+maximum number of conformations with ``bad'' overlaps allowed to appear in a
+row in a single MCM iteration.
+
+\item{DISTCHAINMAX} -- (multi-chain capacity only) maximum distance between the
+ last residue of a given chain and the first residue of the
+ next chain such that restraints will not be imposed; quartic
+ restraints will be imposed for greater distances.
+
+\item{ENERGY\_DEC} -- detailed energies will be printed for each interacting pair
+ or each virtual bond, virtual-bond angle and dihedral angle,
+ side chain, etc. DO NOT use unless a single energy evaluation
+ was requested.
+\end{description}
+
+\subsubsection{Minimizer options}
+
+This data section is in data list format and is read in the READ\_MINIM subroutine.
+
+This data group is present, if MINIMIZE was specified on the control card.
+Otherwise, it must not appear.
+
+\begin{description}
+
+\item{CART} -- minimize in virtual-bond vectors instead of angles.
+
+\item{MAXMIN=number} (integer) (2000)
+maximum number of iterations of the SUMSL minimizer.
+
+\item{MAXFUN=number} (integer) (5000)
+maximum number of function evaluations in a single minimization.
+
+\item{TOLF=number} (real) (1.0e-2)
+Tolerance on function.
+
+\item{RTOLF=number} (real) (1.0d-4)
+Relative tolerance on function.
+
+\item{PRINT\_INI} -- turns on printing nondefault minimization parameters,
+initial variables, and gradients in the SUMSL procedures.
+
+\item{PRINT\_FINAL} -- turns on printing final variables and gradients in
+SUMSL.
+
+\item{PRINT\_STAT} -- turns on printing abbreviated minimization protocol.
+
+\end{description}
+
+The SUMSL minimizer is used in UNRES/CSA. For detailed description of
+the control parameters see the source file cored.f and sumsld.f
+
+
+\subsubsection{CSA control parameters}
+\label{sect:input:main:CSA}
+
+This data group should be present only, if CSA was specified on the control
+card. It is recommended that the readers to read publications on CSA method
+for more complete description of the parameters. Brief description of
+parameters:
+
+\begin{description}
+
+\item{NCONF=number} (integer) (50)
+This corresponds to the size of the bank at the beginning of the
+CSA procedure. The size of the bank, nbank, is set to nconf.
+If necessary (at much later stages of the CSA: see icmax below),
+nbank increases by multiple of nconf.
+
+\item{JSTART=number} (integer) (1)
+
+\item{JEND}=number (integer) (1)
+This corresponds to the limit values of do loop, each of which
+corresponds to an separate CSA run. If jstart=1, and jstart=100,
+this routine will repeat 100 separate CSA runs (limited by CPU)
+each one with separate random number initialization.
+The only difference between two CSA runs (one with jstart=jend=1
+and another one with jstart=jend=2) would be different random
+number initializations if other parameters are identical.
+
+\item{NSTMAX=number} (integer) (500000)
+This is to set a limit the total number of local minimizations of CSA
+before termination.
+
+\end{description}
+
+N1=number (integer) (6)\\
+N2=number (integer) (4)\\
+N3=number (integer) (0)\\
+N4=number (integer) (0)\\
+N5=number (integer) (0)\\
+N6=number (integer) (10)\\
+N7=number (integer) (0)\\
+N8=number (integer) (0)\\
+N9=number (integer) (0)\\
+IS1=number (integer) (1)\\
+IS2=number (integer) (8)\\
+
+These numbers are used to generate trial conformations for each seed.
+See the file newconf.f for more details.
+
+\begin{description}
+ \item{n1:} the total number of trial conformations for each seed by substituting
+ nran number of variable angles (see subroutine newconf1ab and
+ subroutine newconf1ar),
+ \item{n2:} the total number of trial conformations for each seed by substituting
+ nran number of groups of variable angles (see subroutine newconf1bb and
+ subroutine newconf1br),
+ \item{n3:} the total number of trial conformations for each seed by substituting
+ a window of residues which forms a $\beta$-hairpin, if there is no enough
+ $\beta$-hairpins uses the same algorithm as n6,
+ \item{n4:} the total number of trial conformations for each seed by shifting the
+ turn in $\beta$-hairpin by +/- 1 or 2 residues, if there is no enough
+ $\beta$-hairpins uses the same algorithm as n6,
+ \item{n5:} not used,
+ \item{n6:} the total number of trial conformations for each seed by substituting
+ a window of residues [is1,is2] inclusive. The size of the window is
+ determined in a random fashion (see subroutine newconf\_residue for
+ generation of the trial conformations),
+ \item{n7:} the total number of trial conformations for each seed by copying a
+ remote strand pair forming nonlocal $\beta$-sheet contact,
+ \item{n8:} the total number of trial conformations for each seed by copying an
+ $\alpha$-helical segment,
+ \item{n9:} the total number of trial conformations for each seed by shifting the
+ $\alpha$-helical segment by +/- 1 or 2 residues.
+\end{description}
+
+Typical values used for a 75-residue helical protein is
+(6 4 0 0 0 10 1 26) for (n1,n2,n3,n4,n5,n6,is1,is2), respectively.
+In this example, a total of 20 trial conformations are generated for a seed
+Usually is1=1 is used for all applications, and the value of is2 is set about
+to 1/3 of the total number of residues. n3, n4 and n7 are design to help in
+case of proteins with $\beta$-sheets
+
+NRAN0=number (integer) (4)\\
+NRAN1=number (integer) (2)\\
+IRR=number (integer) (1)\\
+
+These numbers are used to determine if the CSA stage is very early.
+One can use (4 2 1) for these values. For more details one should look into
+the file, newconf.f, for more details.
+
+NTOTAL=number (integer) (10000)\\
+CUT1=number (real) (2.0)\\
+CUT2=number (real) (5.0)\\
+
+Annealing schedule is set in following fashion.
+The value of D\_cut is reduced geometrically from 1/cut1 of D\_ave (at the
+beginning) to 1/cut2 of D\_ave (after ntotal number of minimizations) where
+D\_ave is the average distance between two conformations in the First\_bank.
+
+\begin{description}
+
+\item{ESTOP=number} (real) (-3000.0)
+The CSA procedure stops if a conformations with energy lower than estop is
+obtained. If the do-loop set by jstart and jend requires more than one loop,
+the program will go on until the do-loop is finished.
+
+\item{ICMAX=number} (integer) (3)
+The maximum value of cycle (see the original publications for details).
+If the number of cycle exceeds this value the program will add nconf
+more conformations to Bank and First\_bank to continue CSA procedure if
+the new size of the nbank is within the maximum set by nbankm (see above).
+If the size of nbank exceeds the maximum set by nbankm the CSA procedure
+for this run will stop and next CSA will begin depending on the do-loop
+set by jstart and jend.
+
+\item{IRESTART=number} (integer) (0)
+This tells you if the run is fresh start (irestart=0) or a restart (irestart=1)
+starting from an old results
+
+\item{NDIFF=number} (integer) (2)
+The number of variables use in comparison when structure is added to the
+bank,4 - all angels, 2 - only backbone angles $\gamma$ and $\theta$
+
+\item{NBANKTM=number} (integer) (0)
+The maximum number of structures saved in *.CSA.bankt as history of the run
+Do not use bankt on massively parallel computation as it kills scalability.
+
+\item{DELE=number} (real) (20.0)
+Energy cutoff for bankt.
+
+\item{DIFCUT=number} (real) (720.0)
+Angle cutoff for bankt.
+
+\item{IREF=number} (integer) (0)
+0 - normal run, 1 - local CSA which generates only structures close to the
+reference one read from *.CSA.native.int file.
+
+\item{RMSCUT=number} (real) (4.0)
+CA RMSD cut off used in local CSA
+
+\item{PNCCUT=number} (real) (0.5)
+Percentage of native contact used in local CSA
+
+\item{NCONF\_IN=number} (integer) (0)
+The number of conformation read for the first bank from the input file
+*.intin
+\end{description}
+
+Optionally, the CSA parameters can be read from file INPUT.CSA.in, if
+this file exists. If so, they are read in free format in the following
+order:
+
+nconf\\
+jstart,jend\\
+nstmax\\
+n1,n2,n3,n4,n5,n6,n7,n8,is1,is2\\
+nran0,nran1,irr\\
+nseed\\
+ntotal,cut1,cut2\\
+estop\\
+icmax,irestart\\
+ntbankm,dele,difcut\\
+iref,rmscut,pnccut\\
+ndiff\\
+
+
+\subsubsection{MCM data}
+\label{sect:input:main:MCM}
+
+(Data list format, subroutine MCMREAD.)
+
+This data group is present, if MCM was specified on the control card.
+Otherwise it must not appear.
+
+\begin{description}
+
+\item{MAXACC=number} (integer) (100)
+Maximum number of accepted conformations.
+
+\item{MAXTRIAL=number} (integer) (100)
+Maximum number of unsuccessful trials in a row.
+
+\item{MAXTRIAL\_ITER=number} (integer) (1000)
+Maximum number of unsuccessful trials in a single iteration.
+
+\item{MAXREPM=number} (integer) (200)
+Maximum number of repetitions of the same minimum.
+
+\item{RANFRACT=number} (real) (0.5d0)
+Fraction of chain-rebuild motions.
+
+\item{OVERLAP=number} (real) (1.0d3)
+Bad contact energy criterion.
+
+\item{NSTEPH=number} (integer) (0)
+Number of heating step in adaptive sampling.
+
+\item{NSTEPC=number} (integer) (0)
+Number of cooling step in adaptive sampling.
+
+\item{TMIN=number} (real) (298.0d0)
+Minimum temperature in adaptive-temperature sampling).
+
+\item{TMAX=number} (real) (298.0d0)
+Maximum temperature in adaptive-temperature sampling).
+
+The temperature is changed according to the formula:
+
+T = TMIN*EXP(ISTEPH*(TMAX-TMIN)/NSTEPH) when heating
+
+and
+
+T = TMAX*EXP(-ISTEPC*(TMAX-TMIN)/NSTEPC) when cooling
+
+The default is to use a constant temperature.
+
+\item{NWINDOW=number} (integer) (0)
+Number of windows in which the variables will be perturbed; the windows are
+defined by the numbers of the respective amino-acid residues. If NWINDOW
+is nonzero, after specifying all MCM input the next lines must define the
+windows. Each line looks like this:
+
+winstart winend (free format)
+
+e.g. if NWINDOW=2, the input:
+
+4 10\\
+15 20\\
+
+will mean that only the variables of residues 4-10 and 15-20 will be perturbed.
+However, in general, all variables will be considered in minimization.
+
+\item{PRINT\_MC=number} (0)
+Printout level in MCM. 0 - no intermediate printing, 1 and 2 - moderate
+printing, 3 - extensive printing.
+
+\item{NO\_PRINT\_STAT} -- no output to INPUT\_POTENTIALxxx.stat.
+
+\item{NO\_PRINT\_INT} -- no internal-coordinate output to INPUT\_POTENTIALxxx.int.
+
+\end{description}
+
+\subsubsection{MD data}
+\label{sect:input:main:MD}
+
+(Mixed format; subroutine READ\_MDPAR.)
+
+\begin{description}
+
+\item{NSTEP} (1000000) number of time steps per trajectory.
+
+\item{NTWE} (100) NTWX (1000) frequency of energy and coordinate output, respectively.
+The coordinates are dumped in the pdb or compressed Gromacs (cx) format,
+depending on the next keyword.
+NTWE=0 means no energy dump.
+
+\item{MDPDB} - dump coordinates in the PDB format (cx otherwise)
+
+\item{TRAJ1FILE} only the master processor outputs coordinates. This feature pertains
+ only to REMD/MREMD jobs and overrides NTWX; coordinates are dumped at every
+ exchange in MREMD.
+
+\item{REST1FILE} only the master writes the restart file
+
+\item{DT} (real) (0.1) time step; the unit is ``molecular time unit'' (mtu); 1 mtu = 48.9 fs
+
+\item{DAMAX} (real) (1.0) maximum allowed change of acceleration during a single time step.
+The time step gets scaled down, if this is exceeded.
+
+\item{DVMAX} (real) (20.0) -- maximum allowed velocity (in A/mtu)
+
+\item{EDRIFTMAX} (real) (10.0) -- maximum allowed energy drift in a single MD step (10 kcal/mol)
+
+\item{REST} -- restart flag. The calculation is restarted if present.
+
+\item{LARGE} -- very detailed output. Don't use except for debugging.
+
+\item{PRINT\_COMPON} -- prints energy components.
+
+\item{RESET\_MOMENT} (1000) -- frequency of zeroing out the total angular momentum when
+running Berendsen mode calculations (for Langevin calculations meaningless).
+
+\item{RESET\_VEL}=number (integer) (1000) -- frequency of resetting velocities to values
+from Gaussian distribution.
+
+\item{RATTLE} -- use the RATTLE algorithm (constraint bonds); not yet implemented.
+
+\item{RESPA} -- use the Multiple Time Step (MTS) or Adaptive Multiple Time Step (A-MTS)
+algorithm \cite{rakowski_2006}. Without this flag the variable time step (VTS) \cite{khalili_2005} is run.
+
+\item{NTIME\_SPLIT=number} (integer) (1) -- initial number of time-split steps
+
+\item{MAXTIME\_SPLIT=number} (integer) (64) -- maximum number of time-split step
+
+If NTIME\_SPLIT==MAXTIME\_SPLIT, MTS is run.
+
+\item{R\_CUT=number} (real) (2.0) -- the cut-off distance in splitting the forces into short- and
+long-range in site-site VDW distance units.
+
+\item{LAMBDA} (real) (0.3) -- the transition length (in site-site VDW distance units) between
+short- and long-range forces.
+
+\item{XIRESP} -- flag to use MTS/A-MTS with Nos\'e-Hoover/Nos\'e-Poincar\'e thermostats.
+
+\item{LANG=number} (integer) (0) Langevin dynamics flag:
+
+\begin{description}
+\item{0} -- No explicit Langevin dynamics.
+\item{1} -- Langevin with direct integration of the equations of motion (recommended
+ for Langevin calculations)
+\item{2} -- Langevin calculation with analytical pre-integration of the friction and
+ stochastic part of the equations of motion using an algorithm adapted from TINKER.
+ This is MUCH MORE time- and memory-consuming than 1 and requires compiling without
+ the -DLANG0 flag and enormously increases memory requirements.
+\item{3} -- The stochastic integrator developed by Cicotti and coworkers.
+\item{4} -- for other stochastic integrators (not used at present).
+\end{description}
+
+Note: With the enclosed code, the -DLANG0 compiler flag is included which disables
+LANG=2 and LANG=3
+
+\item{TBF} -- Berendsen thermostat.
+
+\item{TAU\_BATH} (1.0) (units are mtus; 1mtu=48.9 fs) -- constant of the coupling to the thermal bath
+ used with the Berendsen thermostat.
+
+\item{NOSEPOINCARE99} -- the Nose-Poincare thermostat as of 1999 will be used.
+
+\item{NOSEPOINCARE01} -- the Nose-Poincare thermostat as of 2001 will be used.
+
+\item{NOSEHOOVER96} -- the Nose-Hoover thermostat will be used.
+
+\item{Q\_NP=number} (real) (0.1) -- the value of the mass of the fictitious particle in the calculations
+ with the Nose-Poincare thermostat.
+
+\item{T\_BATH} (300.0) (in K) -- temperature of canonical simulation or temperature to generate
+velocities.
+
+\item{ETAWAT} (0.8904) -- viscosity of water (in centipoises).
+
+\item{RWAT} (1.4) -- radius of water molecule (in A)
+
+\item{SCAL\_FRIC=number} (real) (0.02) -- scaling factor of the friction coefficients.
+
+\item{SURFAREA} -- scale friction acting on atoms by atoms' solvent accessible area.
+
+\item{RESET\_FRICMAT=number} (integer) (1000) -- recalculate friction matrix every RESET\_FRICMAT MD steps.
+
+\item{USAMPL} -- restraints on q (see reference 5 for meaning) will be imposed (see section .
+In this case, the next records specify the restraints; these records are
+placed before the list of temperatures or numbers of trajectories.
+
+\item{EQ\_TIME=number} (real) (1.0e4) -- time (in mtus; 1 mtu=48.9 fs) after which restraints
+on q will start to be in force.
+
+\end{description}
+
+If USAMPL has been specified, the following information must be supplied after the
+main MD input data record (subroutine READ\_FRAGMENTS):
+
+Line 1: nset, npair, nfrag\_back (number of sets of restraints, number of restrained
+fragments, number of restrained pairs, number of restrained backbone fragments
+(in terms of $\theta$ and $\gamma$ angles)
+
+For each set of restraints (1, 2,..., nset):
+
+\begin{description}
+
+\item{mset(iset)} -- how many times the set is multiplied.
+
+\item{wfrag(i,iset), ifrag(1,i,iset), ifrag2(2,i,iset),qfrag(i,iset)} --
+weight of the restraint, first and last residue of the fragment, target q value.
+This information is repeated through nfrag.
+
+\item{wpair(i,iset), ipair(1,i,iset), ipair(2,i,iset),qinpair(i,iset)} --
+weight of the restraint, first and second fragment of the pair (according to fragment
+list), target q value. This information is repeated through npair
+
+\item{wfrag\_back(1,i,iset), wfrag\_back(2,i,iset), wfrag\_back(3,i,iset),
+ifrag\_back(1,i,iset),ifrag\_back(2,i,iset)} --
+weight of the restraints on $\theta$ angles, weight on the restraints on $\gamma$ angles,
+weight of the restraints on side-chain rotamers, first residue of the fragment,
+last residue of the fragment. This information is repeated through nfrag\_back.
+
+\end{description}
+
+\subsubsection{REMD/MREMD data}
+label{sect:input:main:MREMD}
+
+(Miced format; subroutine READ\_REMDPAR.)
+
+\begin{description}
+
+\item{NREP} (3) -- number of replicas in a REMD/MREMD run.
+
+\item{NSTEX} (1000) -- number of steps after which exchange is performed in REMD/MREMD
+ runs.
+
+The temperatures in replicas can be specified through
+
+\item{RETMIN} (10.0) -- minimum temperature in a REMD/MREMD run,
+
+\item{RETMAX} (1000.0) -- maximum temperature in a REMD/MREMD run.
+
+\end{description}
+
+Then the range from retmin to retmax is divided into equal segments and
+temperature of the replicas assigned accordingly,
+
+or
+
+\begin{description}
+
+\item{TLIST} means that the NREP temperature of the replicas will be input in the
+next record.
+
+\item{MLIST} numbers of trajectories per each of the NREP temperatures will be
+specified in the record after the list of temperatures; this specifies
+a MREMD run.
+
+\end{description}
+
+Important! The number of processors must be exactly equal to the number of
+trajectories, i.e., NREP for a REMD run or $\sum_i mlist(i)$ for a MREMD run.
+
+\begin{description}
+
+\item{SYNC} -- all trajectories will be synchronized every NSTEX time steps
+(by default, they are not synchronized).
+
+\item{TRAJ1FILE} -- only the master processor outputs coordinates. This feature pertains
+ only to REMD/MREMD jobs and overrides NTWX; coordinates are dumped at every
+ exchange in MREMD.
+
+\item{REST1FILE} -- only the master writes the restart file.
+
+\item{HREMD} -- Hamiltonian replica exchange flag; not only temperatures but also
+sets energy-term weights are exchanged between conformations.
+
+\item{TONLY} -- run a ``fake'' HREMD with many sets of energy-term weights in a
+single run but only temperature exchange.
+
+\end{description}
+
+\subsubsection{Energy-term weights}
+\label{sect:input:main:weights}
+
+(Data list format; subroutine MOLREAD.)
+
+\begin{description}
+
+\item{WLONG=number} (real) (1.0d0) --
+common weight of the U(SC-SC) (side-chain side-chain interaction)
+and U(SC,p) (side-chain peptide-group) term.
+
+\item{WSCC=number} (real) (WLONG) --
+weight of the U(SC-SC) term.
+
+\item{WSCP=number} (real) (WLONG)
+weight of the U(SC-p) term.
+
+\item{WELEC=number} (real) (1.0d0)
+weight of the U(p-p) (peptide-group peptide-group interaction) term.
+
+\item{WEL\_LOC=number} (real) (1.0d0)
+weight of the $U_{el;loc}^3$ (local-electrostatic cooperativity, third-order) term.
+
+\item{WCORRH=number} (real) (1.0d0)
+weight of the U(corr) (cooperativity of hydrogen-bonding interactions, fourth-order) term.
+
+\item{WCORR5=number} (real) (0.0d0) --
+weight of the $U_{el;loc}^5$ (local-electrostatic cooperativity, 5th order
+contributions).
+
+\item{WCORR6=number} (real) (0.0d0) --
+weight of the $U_{el;loc}^6$ (local-electrostatic cooperativity, 6th order
+contributions).
+
+\item{WTURN3=number} (real) (1.0d0) --
+weight of the $U_{turn}^3$ (local-electrostatic cooperativity within 3 residue
+segment, 3rd order contribution).
+
+\item{WTURN4=number} (real) (1.0d0) --
+weight of the $U_{turn}^4$ (local-electrostatic cooperativity within 4 residue
+segment, 4rd order contributions).
+
+\item{WTURN6=number} (real) (1.0d0) --
+weight of the $U_{turn}^6$ (local-electrostatic cooperativity within 6 residue
+segment, 6rd order contributions).
+
+\item{WTOR=number} (real) (1.0d0) --
+weight of the torsional term, $U_{tor}$.
+
+\item{WANG=number} (real) (1.0d0) --
+weight of the virtual-bond angle bending term, $U_b$.
+
+\item{WSCLOC=number} (real) (1.0d0) --
+weight of the side-chain rotamer term, $U_{SC}$.
+
+\item{WSTRAIN=number} (real) (1.0d0) --
+scaling factor of the distance-constrain or disulfide-bond strain energy term.
+
+\item{SCALSCP=number} (real) (1.0d0) --
+scaling factor of $U_{SCp}$; this is an alternative to specifying WSCP; in
+this case WSCP will be calculated as WLONG*SCALSCP.
+
+\item{SCAL14=number} (real) (1.0d0) --
+scaling factor of the 1,4 SC-p interactions.
+
+\item{CUTOFF} (7.0) -- cut-off on backbone-electrostatic interactions to compute 4-
+and higher-order correlations.
+
+\item{DELT\_CORR} (0.5) - thickness of the distance range in which the energy is
+decreased to zero.
+
+\end{description}
+
+The defaults are NOT the recommended values. No ``working'' default values
+have been set, because the force field is still under development. The values
+corresponding to the force fields listed in section 4 are as follows:
+
+CASP3:
+\begin{verbatim}
+WELEC=1.5 WSTRAIN=1.0 WTOR=0.08617 WANG=0.10384 WSCLOC=0.10384 WCORR=1.5 &
+WTURN3=0 WTURN4=0 WTURN6=0 WEL_LOC=0 WCORR5=0 WCORR6=0 SCAL14=0.40 SCALSCP=1.0 &
+CUTOFF=7.00000 WSCCOR=0.0
+\end{verbatim}
+
+ALPHA:
+\begin{verbatim}
+WSC=1.00000 WSCP=0.72364 WELEC=1.10890 WANG=0.68702 WSCLOC=1.79888 &
+WTOR=0.30562 WCORRH=1.09616 WCORR5=0.17452 WCORR6=0.36878 WEL_LOC=0.19508 &
+WTURN3=0.00000 WTURN4=0.55588 WTURN6=0.11539 CUTOFF=7.00000 WCORR4=0.0000 &
+WTORD=0.0 WSCCOR=0.0
+\end{verbatim}
+
+BETA:
+\begin{verbatim}
+WSC=1.00000 WSCP=1.10684 WELEC=0.70000 WANG=0.80775 WSCLOC=1.91939 &
+WTOR=3.36070 WCORRH=2.50000 WCORR5=0.99949 WCORR6=0.46247 WEL_LOC=2.50000 &
+WTURN3=1.80121 WTURN4=4.35377 WTURN6=0.10000 CUTOFF=7.00000 WCORR4=0.00000 &
+WSCCOR=0.0
+\end{verbatim}
+
+ALPHABETA:
+\begin{verbatim}
+WSC=1.00000 WSCP=1.43178 WELEC=0.41501 WANG=0.37790 WSCLOC=0.12880 &
+WTOR=1.98784 WCORRH=2.50526 WCORR5=0.23873 WCORR6=0.76327 WEL_LOC=2.97687 &
+WTURN3=0.09261 WTURN4=0.79171 WTURN6=0.01074 CUTOFF=7.00000 WCORR4=0.00000 &
+WSCCOR=0.0
+\end{verbatim}
+
+CASP5:
+\begin{verbatim}
+WSC=1.00000 WSCP=1.54864 WELEC=0.20016 WANG=1.00572 WSCLOC=0.06764 &
+WTOR=1.70537 WTORD=1.24442 WCORRH=0.91583 WCORR5=0.00607 WCORR6=0.02316 &
+WEL_LOC=1.51083 WTURN3=2.00764 WTURN4=0.05345 WTURN6=0.05282 WSCCOR=0.0 &
+CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
+\end{verbatim}
+
+3P:
+\begin{verbatim}
+WSC=1.00000 WSCP=2.85111 WELEC=0.36281 WANG=3.95152 WSCLOC=0.15244 &
+WTOR=3.00008 WTORD=2.89863 WCORRH=1.91423 WCORR5=0.00000 WCORR6=0.00000 &
+WEL_LOC=1.72128 WTURN3=2.99827 WTURN4=0.59174 WTURN6=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
+\end{verbatim}
+
+4P:
+\begin{verbatim}
+WSC=1.00000 WSCP=2.73684 WELEC=0.06833 WANG=4.15526 WSCLOC=0.16761 &
+WTOR=2.99546 WTORD=2.89720 WCORRH=1.98989 WCORR5=0.00000 WCORR6=0.00000 &
+WEL_LOC=1.60072 WTURN3=2.36351 WTURN4=1.34051 WTURN6=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
+\end{verbatim}
+
+GAB:
+\begin{verbatim}
+WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &
+WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &
+WVDWPP=0.11371 WHPB=1.00000 &
+CUTOFF=7.00000 WCORR4=0.00000
+\end{verbatim}
+
+E0G:
+\begin{verbatim}
+WLONG=1.70905 WSCP=2.18310 WELEC=1.06684 WBOND=1.00000 WANG=1.17536 &
+WSCLOC=0.22070 WTOR=2.65798 WTORD=2.00646 WCORRH=0.23541 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.42789 WTURN3=1.68126 WTURN4=0.75080 WTURN6=0.00000 &
+WVDWPP=0.27044 WHPB=1.00000 WSCP14=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000
+\end{verbatim}
+
+1L2Y\_1LE1:
+\begin{verbatim}
+WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &
+WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &
+WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 &
+CUTOFF=7.00000 WCORR4=0.00000
+\end{verbatim}
+
+\subsubsection{Input and/or reference PDB file name}
+\label{sect:input:main:PDB}
+
+(Text format; subroutine MOLREAD.)
+
+If PDBSTART or PDBREF was specified in the control card, this line contains
+the PDB file name. Trailing slashes to specify the full path are permitted.
+The file name can contain up to 64 characters.
+
+\subsubsection{Amino-acid sequence}
+\label{sect:input:main:sequence}
+
+(Mixed format.)
+
+This data appears, if PDBSTART was not specified, otherwise must not be present
+because the sequence would be taken from the PDB file. The first line contains
+the number of amino-acid residues, including the end groups (free format),
+the next lines contain the sequence in 20(1X,A3) format for the three-letter
+or 80A1 format for the one-letter code. There are two types of end-groups:
+Gly (three-letter code) or G (one-letter code), if an end group contains a full
+peptide bond (e.g., the acetyl N-terminal group or the carboxyamide C-terminal
+group) and D (in the three-letter code) or X (in the one-letter code), if the
+end group does not contain a peptide group (e.g., the NH2 N-terminal end group
+or the COOH C-terminal end group). (Note the Gly or G also denotes the regular
+glycine residue, if found in the middle of a chain).
+In the second case the end group is considered as a ``dummy'' group and serves
+only to define the first (last) virtual-bond dihedral angle $\gamma$ for the
+first (last) full amino-acid residue.
+
+Consider, for example, the Ac-Ala(19)-NHMe polypeptide. The three-letter code
+input will look like this:
+
+\begin{verbatim}
+21
+ Gly Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala
+ Gly
+\end{verbatim}
+
+And the one-letter code input will be:
+
+\begin{verbatim}
+21
+GAAAAAAAAAAAAAAAAAAAG
+\end{verbatim}
+
+If the sequence is changed to NH3(+)-Ala(19)-COO(-), the inputs will look
+like this:
+
+\begin{verbatim}
+21
+ D Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala
+ D
+\end{verbatim}
+
+and
+
+\begin{verbatim}
+21
+XAAAAAAAAAAAAAAAAAAAX
+\end{verbatim}
+
+The sequence input is case-insensitive, because the present version of UNRES
+considers each amino-acid residue as an L-residue (there are no torsional
+parameters for the combinations of the D- and L-residues yet). Furthermore,
+each peptide group is considered as a trans group.
+
+If the version of UNRES has multi-chain capacity, placing a dummy residue
+inside the sequence indicates start of a new chain. For example, a system
+composed of two Ala(10) chains can be specified as follows (3-letter code):
+
+\begin{verbatim}
+23
+ D Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala D Ala Ala Ala Ala Ala Ala Ala Ala
+ Ala Ala D
+\end{verbatim}
+
+or (1-letter code)
+
+\begin{verbatim}
+23
+XAAAAAAAAAAXAAAAAAAAAAX
+\end{verbatim}
+
+\subsubsection{Disulfide-bridge information}
+\label{sect:input:main:disulphide}
+
+(Free format; subroutine READ\_BRIDGE.)
+
+1st line:
+
+NS,(ISS(i),i=1,NS)
+
+\begin{description}
+
+\item{NS} -- the number of half-cystines (required even if no half-cystines are present).
+
+\item{ISS(i)} -- the position of ith half-cystine in the sequence (starting from the
+N-terminal end group)
+
+\end{description}
+
+Next line(s) (present only, if $ns>0$ and must not appear otherwise):
+
+NSS,(IHPB(i),JHPB(i),i=1,NSS)
+
+\begin{description}
+
+\item{NSS} -- the number of disulfide bridges; must not be greater than NS/2.
+
+\item{IHPB(i),JHPB(i)} -- the cystine residue forming the ith bridge.
+
+\end{description}
+
+The program will check, whether the residues specified in the ISS list
+are cystines and terminate with error, if any of them is not. The program
+also checks, if the numbers from the IHPB and the JHPB lists have appeared
+in the ISS list.
+
+\subsubsection{Dihedral-angle restraint data}
+\label{sect:input:main:dihedral-restraints}
+
+(Free format; subroutine MOLREAD.)
+
+This set of data specifies the harmonic constraints (if any) imposed on selected
+virtual-bond dihedral angles $\gamma$.
+
+1st line:
+
+\begin{description}
+
+\item{NDIH\_CONSTR} -- the number of restrained $\gamma$ angles (required even if no
+restrains are applied).
+
+\end{description}
+
+2nd line (present only, if NDIH\_CONSTR$>$0; must not appear otherwise):
+FTORS - the force constant expressed in kcal/(mol*rad**2)
+
+next NDIH\_CONSTR lines (present only, if NDIH\_CONSTR$>$0):
+
+IDIH\_CONSTR(i),PHI0(i),DRANGE(i)
+
+\begin{description}
+
+\item{IDIH\_CONSTR(i)} -- the number of ith restrained $\gamma$ angle. The angles are
+numbered after the LAST $\alpha$-carbons. Thus, the first ``real'' angle has number
+4 and it corresponds to the rotation about the CA(2)-CA(3) virtual-bond axis
+and the last angle has the number NRES and corresponds to the rotation about
+the CA(NRES-2)-CA(NRES-1) virtual-bond axis.
+
+\item{PHI0(i)} -- the ``center'' of the restraint (expressed in degrees).
+
+\item{DRANGE(i)} -- the ``flat well'' range of the restraint (in degrees).
+
+\end{description}
+
+The restraint energy for the ith restrained angle is expressed as:
+
+\begin{displaymath}
+E_{dih} = \begin{cases}
+\rm FTORS\times(\gamma_{IDIH\_CONSTR(i)}-PHI0(i)+DRANGE(i))^2&\mbox{if}\ \ \rm \gamma_{IDIH\_CONSTR(i)}\\
+ &<PHI0(i)+DRANGE(i)\\
+\\
+0 &\rm if\ \ PHI0(i)-DRANGE(i) \\
+ &\le \gamma_{IDIH\_CONSTR(i)} \\
+ &\le PHI0(i)+DRANGE(i)\\
+\\
+\rm FTORS\times(\gamma_{IDIH\_CONSTR(i)}-PHI0(i)+DRANGE(i))^2&\mbox{if}\ \ \rm \gamma_{IDIH\_CONSTR(i)}\\
+ &>PHI0(i)+DRANGE(i)
+\end{cases}
+\end{displaymath}
+
+Applying dihedral-angle constraints also implies that for ith constrained
+$\gamma$ angle the sampling be carried out from the
+[PHI0(i)-DRANGE(i)..PHI0(i)+DRANGE(i)] interval and not from the $[-\pi..\pi]$
+interval, if random conformations are generated. If only this and not
+restrained minimization is required, just set FTORS to 0.
+
+\subsubsection{Distance restraints}
+\label{sect:input:main:disance-restraints}
+
+(Mixed format; subroutine READ\_DIST\_CONSTR.)
+
+Restraints are imposed on C$^\alpha\cdots$C$^\alpha$ SC$\cdots$SC distances (C$^\beta\cdots$C$^\beta$.
+
+\begin{description}
+
+\item{NDIST=number} (integer) (0) -- number of restraints on specific distances.
+
+\item{NFRAG=number} (integer) (0) -- number of distance-restrained protein segments.
+
+\item{NPAIR=number} (integer) (0) -- number of distance-restrained pairs of segments.
+ Specifying NPAIR requires specification of segments.
+
+\item{IFRAG=start(1),end(1),start(2),end(2)...start(NFRAG),end(NFRAG)} (integers) --
+First and last residues of the distance restrained segments.
+
+\item{WFRAG=w(1),w(2),...,w(NFRAG) (reals)} -- force constants or bases for force
+constant calculation corresponding to fragment restraints.
+
+\item{IPAIR=start(1),end(1),start(2),end(2),...,start(NPAIR),end(NPAIR)} (integers)
+-- numbers of segments (consecutive numbers of start or end pairs in IFRAG
+specification), the distances between which will be restrained.
+
+\item{WPAIR=w(1),w(2),...,w(NFRAG)} (reals) -- force constants or bases for force
+constant calculation corresponding to pair restraints.
+
+\item{DIST\_CUT=number} (real) (5.0) -- the cut-off distance in angstroms for force-
+constant calculations.
+
+The force constants within fragments/between pairs of fragments are calculated
+depending on the value of DIST\_CONSTR described in section 5.1:
+
+\begin{description}
+
+\item{1} -- all force constants are equal to the respective entries of WFRAG/WPAIR
+
+\item{2} -- the force constants are equal to the respective entries of WFRAG/WPAIR
+ when the distance between the C$^\alpha$ atoms in the reference structure
+ $\le$D\_CUT, 0 otherwise.
+
+\item{3} -- the force constants are calculated from the formula:
+
+\end{description}
+
+\item{$k(C^\alpha_j,C^\alpha_k)=W\times\exp{-[d(C^\alpha_j,C^\alpha_k)/DIST\_CUT)]^2/2}$}
+
+where $k(C^\alpha_j,C^\alpha_k)$ is the force constant between the respective C$^\alpha$ atoms,
+$d(C^\alpha_j,C^\alpha_k)$ is the distance between these C$^\alpha$ atoms in the reference
+structure, and W is the basis for force-constant calculation (see above).
+
+\end{description}
+
+The above restraints are harmonic resatraints of the form
+
+\begin{displaymath}
+E_{dis} = \sum_i k_i \left(d_i - d_i^{ref}\right)^2
+\end{displaymath}
+
+where $d_i$ is the distance in the calculated structure and $d_i^{ref}$ is the respective
+distance in the reference (PDB) structure. The reference structure is required.
+
+If NDIST$>$0, the restraints on specific distance are input explicitly (no reference structure is requires).
+The restraints are quartic restraints of a similar form as that in section
+\ref{sect:input:main:dihedral-restraints} but with angles replaced with distances.
+
+ihpb(i), jhpb(i), dhpb(i), dhpb1(i), ibecarb(i), forcon(i), i=1,NDIST
+
+\begin{description}
+
+\item{ihpb(i)} and jhpb(i) are the numbers of the residues the distance
+between the C$^\alpha$ atoms of which will be distance restrained,
+
+\item{dhpb(i)} and dhpb1(i) are the lower and upper distance-restraint,
+
+\item{ibecarc(i)} is the restraint-type flag;
+ibecarb(i)==0 indicates that the restraints are imposed on the
+C$^\alpha\cdots$C$^\alpha$ distances; otherwise restraints on the
+SC$\cdots$SC distances are imposed,
+
+\item{forcon(i)}
+is the respective force constant.
+
+\end{description}
+
+\subsubsection{Internal coordinates of the reference structure}
+\label{sect:input:main:internalref}
+
+(Free format; subroutine READ\_ANGLES.)
+
+This part of the data is present, if REFSTR, but not PDBREF was specified,
+otherwise must not appear. It contains the following group of variables:
+
+\begin{description}
+\item{(THETA(i),i=3,NRES)} -- the virtual-bond valence angles THETA.
+\item{(PHI(i),i=4,NRES)} -- the virtual-bond dihedral angles GAMMA.
+\item{(ALPH(i),i=2,NRES-1)} -- the ALPHA polar angles of consecutive side chains.
+\item{(OMEG(i),i=2,NRES-1)} -- the BETA polar angles of consecutive side chains.
+\end{description}
+
+ALPHA(i) and OMEG(i) correspond to the side chain attached to CA(i). THETA(i)
+is the CA(i-2)-CA(i-1)-CA(i) virtual-bond angle and PHI(i) is the
+CA(i-3)-CA(i-2)-CA(i-1)-CA(i) virtual-bond dihedral angle $\gamma$.
+
+\subsubsection{Internal coordinates of the initial conformation}
+\label{sect:input:main:intcoord}
+
+(Free format; subroutine READ\_ANGLES.)
+
+This part of the data is present, if RAND\_CONF, MULTCONF, THREAD, or PDBSTART
+were not specified, otherwise must not appear. This input is as in section \ref{sect:support}.
+
+\paragraph{File name with internal coordinates of the conformations to be processed}
+\label{sect:input:main:intcord:files}
+
+(Text format; subroutine MOLREAD.)
+
+This data is present only, if MULTCONF was specified. It contains the name of
+the file with the internal coordinates. Up to 64 characters are allowed.
+The structure of the file is that of the *.int file produced by UNRES/CSA.
+See section ``The structure of the INT files'' for details.
+
+\subsubsection{Control data for energy map construction}
+\label{sect:input:main:map}
+
+(Data list format; subroutine MAP\_READ.)
+
+These data lists appear, if NMAP=n was specified, where n is the number of
+variables that will be grid-searched. One list is per one variable or a
+group of variables set equal (see below):
+
+\begin{description}
+\item{PHI} -- the variable is a virtual-bond dihedral angle $\gamma$.
+\item{THE} -- the variable is a virtual-bond angle $\theta$.
+\item{ALP} -- the variable is a side-chain polar angle $\alpha$.
+\item{OME} -- the variable is a side-chain polar angle $\beta$.
+\end{description}
+
+\begin{description}
+\item{RES1=number} (integer)
+\item{RES2=number} (integer)
+\end{description}
+
+The range of residues for which the values will be set; all these variables
+will be set at the same value. It is required that RES2$>$RES1.
+
+\begin{description}
+\item{FROM=angle} (real)
+\item{TO=angle} (real)
+\end{description}
+
+Lower and upper limit of scanning in grid search (in degrees)
+
+\begin{description}
+\item{NSTEP=number} (integer)
+\end{description}
+
+Number of steps in scanning along this variable/group of variables.
+
+\subsection{Input coordinate files}
+\label{sect:input:coordfiles}
+
+(Text format; subroutine MOLREAD.)
+
+At present, geometry can be input either from the external files in the PDB
+format (with the PDBSTART option) or multiple conformations can be read
+as virtual-bond-valence and virtual-bond dihedral angles when the MULTCONF
+option is used (the latter, however, implies using standard virtual-bond
+lengths as initial values). The structure of internal-coordinate files
+is the same as that of output internal-coordinate files described in section
+9.1.1.
+
+\subsection{Other input files}
+\label{sect:input:otherfiles}
+
+CSA parameters can optionally be read in free format from file INPUT.CSA.in
+(see section 8.1.4). When a CSA run is restarted, the CSA-specific output files
+also serve as input files. INPUT is the prefix of input and output files
+as explained in section \ref{sect:command}.
+
+Restart files for MD and REMD simulations. They are read when the keyword
+RESTART appears on the MD/REMD data group (section \ref{sect:input:main:MD}).
+
+\newpage
+
+\section{OUTPUT FILES}
+\label{sect:output}
+
+UNRES ``main'' output files (INPUT.out\_\$\{POT\}[processor]) are log files from
+a run. They contain the information of the molecule, force field, calculation
+type, control parameters, etc.; however, not the structures produced during
+the run or their energies except single-point energy evaluation and
+minimization-related runs. The structural information is included in
+coordinate files (*.int, *.x, *.pdb, *.mol2, *.cx) and statistics files (*.stat),
+respectively; these files are further processed by other programs (WHAM,
+CLUSTER) or can be viewed by molecular viewers (pdb or mol2 files).
+
+\subsection{Coordinate files}
+\label{sect:output:coord}
+
+\subsubsection{The internal coordinate (INT) file}
+\label{sect:output:coord:int}
+
+This file contains the internal coordinates of the conformations produced
+by UNRES in non-MD runs. The virtual-bond lengths are assumed constant so
+only the angular variables are provided.
+
+IT,ENER,NSS,(IHPB(I),JHPB(I),I=1,NSS)\\
+(I5,F12.5,I2,9(1X,2I3))
+
+\begin{description}
+\item{IT} -- the number of the conformation.
+\item{ENER} -- total energy.
+\item{NSS} -- the number of disulfide bridges.
+\item{(IHPB(I),JHPB(I),I=1,NSS)} -- the positions of the pairs of half-cystines .
+forming the bridges. If NSS$>9$9, the remaining pairs are written in the
+following lines in the (3X,11(1X,2I3)) format.
+\end{description}
+
+(THETA(I),I=3,NRES)\\
+(8F10.4)
+
+The virtual-bond angles THETA (in degrees)
+
+(PHI(I),I=4,NRES)\\
+(8F10.4)
+
+The virtual-bond dihedral angles GAMMA (in degrees)
+
+(ALPH(I),I=2,NRES-1)\\
+(OMEG(I),I=2,NRES-1)\\
+(8F10.4)
+
+The polar angles ALPHA and BETA of the side-chain centers (in degrees).
+
+\subsubsection{The plain Cartesian coordinate (X) files}
+\label{sect:output:coord:cart}
+
+(Subroutine CARTOUT.)
+
+This file contains the Cartesian coordinates of the $\alpha$-carbon and
+side-chain-center coordinates. All conformations from an MD/MREMD
+trajectory are collated to a single file. The structure of each
+conformation's record is as follows:
+
+1st line: time, potE, uconst, t\_bath,nss, (ihpb(j), jhpb(j), j=1,nss),
+nrestr, (qfrag(i), i=1,nfrag), (qpair(i), i=1,npair),
+(utheta(i), ugamma(i), uscdiff(i), i=1,nfrag\_back)
+
+\begin{description}
+\item{time:} MD time (in ``molecular time units'' 1 mtu = 4.89 fs),
+\item{potE:} potential energy,
+\item{uconst:} restraint energy corresponding to restraints on Q and backbone geometry,
+(see section \ref{sect:input:main:MD}),
+\item{t\_bath:} thermostat temperature,
+\item{nss:} number of disulfide bonds,
+\item{ihpb(j), jhpb(j):} the numbers of linked cystines for jth disulfide bond,
+\item{nrestr:} number of restraints on q and local geometry,
+\item{qfrag(i):} q value for ith fragment,
+\item{qpair(i):} q value for ith pair,
+\item{utheta(i):} sum of squares of the differences between the theta angles
+ of the current conformation from those of the experimental conformation,
+\item{ugamma(i):} sum of squares of the differences beaten the gamma angles
+ of the current conformation from those of the experimental conformation,
+\item{uscdiff(i):} sum of squares of the differences between the Cartesian difference
+ of the unit vector of the C$^\alpha$-SC axis of the current conformation from
+ those of the experimental conformation.
+\end{description}
+
+Next lines: Cartesian coordinates of the C$^\alpha$ atoms (including dummy atoms)
+(sequentially, 10 coordinates per line)
+Next lines: Cartesian coordinates of the SC atoms (including glycines and
+dummy atoms) (sequentially, 10 coordinates per line)
+
+\subsubsection{The compressed Cartesian coordinate (CX) files}
+\label{sect:output:coord:cx}
+
+These files are compressed binary files (extension cx). For each conformation,
+the items are written in the same order as specified in section \ref{sect:output:coord:cx}. For
+MREMD runs, if TRAJ1FILE is specified on MREMD record (see section \ref{sect:input:main:MD}),
+snapshots from all trajectories are written every time the coordinates
+are dumped. Thus, the file contains snapshot 1 from trajectory 1, ...,
+snapshot 1 from trajectory M, snapshot 2 from trajectory 1, ..., etc.
+
+The compressed cx files can be converted to pdb file by using the xdrf2pdb
+auxiliary program (single trajectory files) or xdrf2pdb-m program (multiple
+trajectory files from MREMD runs generated by using the TRAJ1FILE option).
+The multiple-trajectory cx files are also input files for the auxiliary
+WHAM program.
+
+\subsubsection{The Brookhaven Protein Data Bank format (PDB) files}
+\label{sect:output:coord:PDB}
+
+(Subroutine PDBOUT.)
+
+\sloppy
+These files are written in PDB standard (see. e.g.,
+\href{ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf}{\textcolor{blue}{ftp://ftp.wwpdb.org/pub/pdb\-/doc/\-format\_descriptions}}). %\-/Format\_v33\_Letter.pdf}.
+The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used.
+The C$^\alpha$ (marked CA) and SC (marked CB) coordinates are output. The CONECT
+records specify the C$^\alpha\cdots$C$^\alpha$ and C$^\alpha\cdots$SC virtual bonds. Secondary
+structure is detected based on peptide-group contacts, as specified in
+ref 12. Dummy residues are omitted from the output. If the program has
+multiple-chain function, the presence of a dummy residue in a sequence
+starts a new chain, which is assigned the next alphabet letter as ID, and
+residue numbering is started over.
+
+\subsubsection{The SYBYLL (MOL2) files}
+\label{sect:output:coord:subyll}
+
+See the description of mol2 format (e.g.,
+\href{http://tripos.com/data/support/mol2.pdf}{http://tripos.com/data/support/mol2.pdf}.
+Similar remarks apply as for
+the PDB format (section \ref{sect:output:coord:PDB}).
+
+\subsection{The summary (STAT) file}
+
+\subsubsection{Non-MD runs}
+
+This file contains a short summary of the quantities characterizing the
+conformations produced by UNRES/CSA. It is created for MULTCONF and MCM.
+
+NOUT,EVDW,EVDW2,EVDW1+EES,ECORR,EBE,ESCLOC,ETORS,ETOT,RMS,FRAC\\
+(I5,9(1PE14.5))
+
+\begin{description}
+\item{NOUT} -- the number of the conformations
+\item{EVDW,EVDW2,EVDW1+EES,ECORR,EBE,ESCLOC,ETORS} -- energy components
+\item{ETOT} -- total energy
+\item{RMS} -- RMS deviation from the reference structure (if REFSTR was specified)
+\item{FRAC} -- fraction of side chain - side chain contacts of the reference
+ structure present in this conformation (if REFSTR was specified)
+\end{description}
+
+\subsubsection{MD and MREMD runs}
+\label{sect:output:coord:MD}
+
+Each line of the stat file generated by MD/MREMD runs contains the following
+items in sequence:
+
+\begin{description}
+\item{step} -- the number of the MD step
+\item{time} -- time [unit is MTU (molecular time unit) equal to 48.9 fs]
+\item{Ekin} -- kinetic energy [kcal/mol]
+\item{Epot} -- potential energy [kcal/mol]
+\item{Etot} -- total energy (Ekin+Epot)
+\item{H-H0} -- the difference between the cureent and initial extended Hamiltionian
+ in Nose-Hoover or Nose-Poincare runs; not present for other thermostats.
+\item{RMSD} -- root mean square deviation from the reference structure (only in
+ REFSTR has been specified)
+item{damax} -- maximum change of acceleration between two MD steps
+\item{fracn} -- fraction of native side-chain concacts (very crude, based on
+ SC-SC distance only)
+\item{fracnn} -- fraction of non-native side-chain contacts
+\item{co} -- contact order
+\item{temp} -- actual temperature [K]
+\item{T0} -- initial (microcanonical runs) or thermostat (other run types)
+ temperature [K]
+\item{Rgyr} -- radius of gyration based on C$^\alpha$ coordinates [A]
+\item{proc} -- in MREMD runs the number of the processor (the number of the
+ trajectory less 1); not present for other runs.
+\end{description}
+
+For an USAMPL run, the following items follow the above list:
+
+\begin{description}
+\item{iset} -- the number of the restraint set
+\item{uconst} -- restraint energy pertaining to q-values
+\item{uconst\_back} -- restraint energy pertaining to virtual-backbone restraints
+\item{(qfrag(i),i=1,nfrag)} -- q values of the specified fragments
+\item{(qpair(ii2),ii2=1,npair)} -- q values of the specified pairs of fragments
+\item{(utheta(i),ugamma(i),uscdiff(i),i=1,nfrag\_back)} -- virtual-backbone and
+ side-chain-rotamer restraint energies of the fragments specified
+\end{description}
+
+If PRINT\_COMPON has been specified, the energy components are printed
+after the items described above.
+
+\subsection{CSA-specific output files}
+\label{sect:output:coord:CSA}
+
+There are several output files from the CSA routine:
+INPUT.CSA.seed, INPUT.CSA.history, INPUT.CSA.bank, INPUT.CSA.bank1,
+INPUT.CSA.rbank INPUT.CSA.alpha, INPUT.CSA.alpha1.
+
+The most informative outfile is INPUT.CSA.history. This file first write down
+the parameters in INPUT.CSA.csa file. Later it shows the energies of random
+minimized conformations in its generation. After sorting the First\_bank
+in energy (ascending order), the energies of the First\_bank is re-written here.
+After this the output looks like:
+
+\begin{verbatim}
+ 1 0 100 6048.2 1 100-224.124-114.346 202607 100 100
+ 1 0 700 5882.6 2 29-235.019-203.556 1130308 100 100
+ 1 0 1300 5721.5 2 18-242.245-212.138 2028008 100 100
+ 1 0 1900 5564.8 13 54-245.185-218.087 2897988 98 100
+ 1 0 2500 5412.4 13 61-246.214-222.068 3706478 97 100
+ 1 0 3100 5264.2 13 89-248.715-224.939 4514196 96 100
+\end{verbatim}
+
+Each line is written between each iteration (just after selection
+of seed conformations) containing following data:
+jlee,icycle,nstep,cutdif,ibmin,ibmax,ebmin,ebmax,nft,iuse,nbank
+ibmin and ibmax lists the index of bank conformations corresponding to the
+lowest and highest energies with ebmin and ebmax.
+nft is the total number of function evaluations so far.
+iuse is the total number of conformations which have not been used as seeds
+prior to calling subroutine select\_is which select seeds.
+
+Therefore, in the example shown above, one notes that so far 3100
+minimizations has been performed corresponding to the total of 4514196
+function evaluations. The lowest and highest energy in the Bank is
+-248.715 (\#13) and -224.939 (\#89), respectively. The number of conformations
+already used as seeds (not including those selected as seeds in this iteration)
+so far is 4 (100-96).
+
+The files INPUT.CSA.bank and INPUT.CSA.rbank contains data of Bank and
+First\_bank. For more information on these look subroutines write\_bank
+and write\_rbank. The file INPUT.CSA.bank is overwritten between each
+iteration whereas Bank is accumulated in INPUT.CSA.bank1 (not for every
+iteration but as specified in the subroutine together.f).
+
+The file INPUT.CSA.seed lists the index of the seed conformations with their
+energies. Files INPUT.CSA.alpha, INPUT.CSA.alpha1 are written only once
+at the beginning of the CSA run. These files contain some arrays used
+in CSA procedure.
+
+\newpage
+
+\section{TECHNICAL SUPPORT CONTACT INFORMATION}
+\label{sect:support}
+
+ Dr. Adam Liwo\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
+ phone: +48 58 523 5430\\
+ fax: +48 58 523 5472\\
+ e-mail: \href{mailto:adam@chem.univ.gda.pl}{adam@chem.univ.gda.pl}\\
+
+ Dr. Cezary Czaplewski\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
+ phone: +48 58 523 5430\\
+ fax: +48 58 523 5472\\
+ e-mail: \href{mailto:czarek@chem.univ.gda.pl}{czarek@chem.univ.gda.pl}\\
+
+ Dr. Stanislaw Oldziej\\
+ Intercollegiate Faculty of Biotechnology\\
+ University of Gdansk, Medical University of Gdansk\\
+ ul. Kladki 22, 80-922 Gdansk, Poland\\
+ phone: +48 58 523 5361\\
+ fax: +48 58 523 5472\\
+ e-mail: \href{mailto:stan@biotech.ug.gda.pl}{stan@biotech.ug.gda.pl}\\
+
+ Dr. Jooyoung Lee\\
+ Korea Institute for Advanced Study\\
+ 207-43 Cheongnyangni 2-dong, Dongdaemun-gu,\\
+ Seoul 130-722, Korea\\
+ phone: +82-2-958-3890\\
+ fax: +82-2-958-3731\\
+ email: \href={mailto:jlee@kias.re.kr}{jlee@kias.re.kr}
+
+\small{
+ Prepared by Adam Liwo and Jooyoung Lee, 7/17/99\\
+ Revised by Cezary Czaplewski 1/4/01\\
+ Revised by Cezary Czaplewski and Adam Liwo 8/26/03\\
+ Revised by Cezary Czaplewski and Adam Liwo 11/26/11\\
+ Revised by Adam Liwo 02/19/12\\
+ LaTeX version by Adam Liwo 09/25/12
+}
+\end{document}
--- /dev/null
+\documentclass[12pt]{article}
+%\usepackage{latex2html}
+\usepackage{enumerate}
+\usepackage{longtable}
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{color}
+\parindent=0pt
+\parskip=12pt
+\textheight=24cm
+\textwidth=18cm
+\topmargin=-2.5cm
+\oddsidemargin=-0.5cm
+\setcounter{secnumdepth}{5}
+\setcounter{tocdepth}{5}
+\begin{document}
+\sloppy
+
+\title{WHAM \\ (Weighted Histogram Analysis Method)\\
+ Processing results of UNRES/MREMD simulations}
+
+\author{Department of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Sobieskiego 18\\ 80-952 Gdansk, Poland\\
+\\
+\\
+Scheraga Group\\ Baker Laboratory of Chemistry \\
+and Chemical Biology\\ Cornell University\\ Ithaca, NY 14853-1303, USA}
+
+\maketitle
+
+\newpage
+
+\tableofcontents
+
+%1. License terms
+%2. References
+%3. Functions of the program
+%4. Installation
+%5. Running the program
+%6. Input and output files
+%6.1. Summary of files
+%6.2. The main input file
+%6.2.1. General data
+%6.2.2. Molecule and energy parameter data
+%6.2.2.1. General information
+%6.2.2.2. Sequence information
+%6.2.2.3. Dihedral angle restraint information
+%6.2.2.4. Disulfide-bridge data
+%6.2.3. Energy-term weights and parameter files
+%6.2.4. (M)REMD/Hamiltonian (M)REMD setting specification
+%6.2.5. Information of files from which to read conformations
+%6.2.6. Information of reference structure and comparing scheme
+%6.3. The structure of the main output file (out)
+%6.4. The thermodynamic quantity and ensemble average (stat) files
+%6.5. The conformation summary with classification (stat) files
+%6.6. The histogram files
+%6.7. The rmsd-radius of gyration potential of mean force files
+%6.8. The PDB files
+%6.9. The compresses Cartesian coordinates (cx) file
+%7. Support
+
+\newpage
+
+\section{LICENSE TERMS}
+\label{sect:license}
+
+\begin{itemize}
+
+\item
+ This software is provided free of charge to academic users, subject to the condition that no part of it be sold or used otherwise for commercial purposes, including, but not limited to its incorporation into commercial software packages, without written consent from the authors. For permission contact Prof. H. A. Scheraga, Cornell University.
+
+\item
+ This software package is provided on an ``as is'' basis. We in no way warrant either this software or results it may produce.
+
+\item
+ Reports or publications using this software package must contain an acknowledgment to the authors and the NIH Resource in the form commonly used in academic research.
+
+\end{itemize}
+
+\newpage
+
+\section{REFERENCES}
+\label{sect:references}
+
+Citing the following references in your work that makes use of the WHAM software is gratefully
+acknowledged:
+
+\begingroup
+\renewcommand{\section}[2]{}%
+\begin{thebibliography}{10}
+
+\bibitem{kumar_1992}
+S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, J.M. Rosenberg.
+The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method.
+{\it J. Comput. Chem.}, {\bf 1992}, 13, 1011-1021.
+
+\bibitem{liwo_2007}
+A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, K. Wachucik, H.A. Scheraga.
+Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.
+{\it J. Phys. Chem. B}, {\bf 2007}, 111, 260-285.
+
+\bibitem{oldziej_2004}
+S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 2. Off-lattice tests of the method with single proteins.
+{\it J. Phys. Chem. B}, {\bf 2004}, 108, 16934-16949.
+
+\end{thebibliography}
+
+\endgroup
+
+\newpage
+
+\section{FUNCTIONS OF THE PROGRAM}
+\label{sect:func}
+
+The program processes the results of replica exchange (REMD) or multiplexed replica exchange molecular
+dynamics (MREMD) simulations with UNRES to compute the probabilities of the obtained conformations to
+occur at particular temperatures. The program is based on the variant of the weighted histogram analysis
+(WHAM) method \cite{kumar_1992} described in ref \cite{liwo_2007}.
+
+The program outputs the following information:
+
+\begin{enumerate}[(a)]
+
+\item
+Temperature profiles of thermodynamic and structural ensemble-averaged quantities.
+
+\item
+Histograms of native-likeness measure q (defined by eqs 8-11 of ref [\cite{liwo_2007}]).
+
+\item
+Optionally the most probable conformations at REMD temperatures.
+
+\item
+Optionally the coordinates with information to compute probabilities for the conformations to occur at any temperature.
+
+\end{enumerate}
+
+The program takes usually UNRES compressed coordinate files (cx files) from MREMD obtained by using the TRAJ1FILE option. The user can request to partition the whole run into equal slices (or windows), each starting from, say, snapshot n (for each trajectory) and ending at snapshot n+1.
+Alternatively, the UNRES Cartesian coordinate (x files) can be input; however, they must contain only the analyzed portion of the trajectories; they are usually prepared from single trajectories by using xdrf2x.
+
+Two versions of the program are provided:
+
+\begin{enumerate}[(a)]
+
+\item
+Canonical version which treats single polypeptide chains; the source code is in WHAM/src directory.
+
+\item
+Version for oligomeric proteins; multiple chains are handled by inserting dummy residues in the sequence; the source code is in WHAM/src-M directory.
+
+\end{enumerate}
+
+\newpage
+
+\section{INSTALLATION}
+\label{sect:install}
+
+Customize Makefile to your system. See section 7 of the description of UNRES for compiler flags that are used to created executables for a particular force field. There are already several Makefiles prepared for various systems and force fields.
+
+Run make in the WHAM/src directory WHAM/src-M directory for multichain version. Make sure that MPI is installed on your system; the present program runs only in parallel mode.
+
+\newpage
+
+\section{RUNNING THE PROGRAM}
+\label{sect:running}
+
+The program requires a parallel system to run. Depending on system, either the wham.csh C-shell script (in WHAM/bin directory) can be started using mpirun or the binary in the C-shell script must be executed through mpirun. See the wham.csh C-shell script and section 6 for the files processed by the program.
+
+\newpage
+
+\section{INPUT AND OUTPUT FILES}
+\label{sect:inoutfiles}
+
+\subsection{Summary of the files}
+\label{sect:inoutfiles:summary}
+
+The C-shell script wham.csh is used to run the program (see the WHAM/bin directory). The data files that the script needs are mostly the same as for UNRES (see section 6 of UNRES description). In addition, the environmental variable CONTFUN specifies the method to assess whether two side chains are at contact; if CONTFUN=GB, the criterion defined by eq 8 of ref 4 is used to assess whether two side chains are at contact. Also, the parameter files from the C-shell scripts are overridden if the data from Hamiltonian MREMD are processed; if so, the parameter files are defined in the main input file.
+
+The main input file must have inp extension. If it is INPUT.inp, the output files are as follows:
+
+\begin{description}
+
+\item{INPUT.out\_POTxxx} -- output files from different processors (INPUT.out\_000 is the main output file). POT is the identifier of the sidechain-sidechain potential.
+
+\item{INPUT\_POT\_GB\_xxx.stat} or INPUT\_POT\_slice\_YYXXX.stat -- the summary conformation-classification file from processor xxx (each processor handles part of conformations); the second occurs if the run is partitioned into slices.
+
+\item{INPUT.thermal} or INPUT\_slice\_yy.thermal -- thermodynamic functions and temperature profiles of the ensemble averages (the second form if the run is partitioned into slices).
+
+\item{INPUT\_T\_xxx.pdb} or INPUT\_slice\_yy\_T\_xxx.pdb -- top conformations the number of these conformations is selected by the user) in PDB format.
+
+\item{INPUT.cx} -- the compressed UNRES coordinate file with information to compute the probability of a given conformation at any temperature.
+
+\item{INPUT.hist}, INPUT\_slice\_xx.hist, INPUT\_par\_yy.hist, INPUT\_par\_yy\_slice\_zz.x -- histograms of q at MREMD temperatures.
+
+\item{INPUT.ent}, INPUT\_slice\_xx.ent, INPUT\_par\_yy.ent, INPUT\_par\_yy\_slice\_xx.ent -- the histogram(s) of energy density.
+
+\item{INPUT.rmsrgy}, INPUT\_par\_yy.rmsrgy, INPUT\_slice\_xx.rmsrgy or INPUT\_par\_yy\_slice\_xx.rmsrgy -- the 2D histogram(s) of rmsd from the experimental structure and radius of gyration.
+
+\end{description}
+
+\subsection{Main input file}
+\label{sect:inoutfiles:main}
+
+This file has the same structure as the UNRES input file; most of the data are input in a keyword-based form (see section 7.1 of UNRES description). The data are grouped into records, referred to as lines. Each record, except for the records that are input in non-keyword based form, can be continued by placing an ampersand (\&) in column 80. Such a format is referred to as the data list format.
+
+In the following description, the default values are given in parentheses.
+
+\subsubsection{General data (data list format)}
+\label{sect:inoutfiles:main:general}
+
+\begin{description}
+
+\item{N\_ENE} (N\_ENE\_MAX) -- the number of energy components.
+
+\item{SYM} (1) -- number of chains with same sequence (for oligomeric proteins only).
+
+\item{HAMIL\_REP} -- if present, Hamiltonian process the results of replica exchange runs (replicas with different parameters of the energy function).
+
+\item{NPARMSET} (1) -- number of energy parameter sets ($>$1 only for Hamiltonian replica exchange simulations).
+
+\item{SEPARATE\_PARSET} -- if present, HREMD was run in a mode such that only temperature but not energy-function parameters was exchanged.
+
+\item{IPARMPRINT} (1) -- number of parameter set with which to construct conformational ensembles; important only when HREMD runs are processed.
+
+\item{ENE\_ONLY} -- if present, only conformational energies will be calculated and printed; no WHAM iteration.
+
+\item{EINICHECK} (2) -- $>0$ compare the conformational energies against those stored in the coordinate file(s); 1: compare but print only a warning message if different; 2: compare and terminate the program if different; 0: don't compare.
+
+\item{MAXIT} (5000) -- maximum number of iterations in solving WHAM equations.
+
+\item{ISAMPL} (1) -- input conformation sampling frequency (e.g., if ISAMPL=5, only each 5th conformation will be read).
+
+\item{NSLICE} (1) -- number of ``slices'' or ``windows'' into which each trajectory will be partitioned; each slice will be analyzed independently.
+
+\item{FIMIN} (0.001) -- maximum average difference between window free energies between the current and the previous iteration.
+
+\item{ENSEMBLES} (0) -- number of conformations (ranked according to probabilities) to be output to PDB file at each MREMD temperature; 0 means that no conformations will be output. Non-zero values should not be used when NSLICE$>$1.
+
+\item{CLASSIFY} -- if present, each conformation will be assigned a class, according to the scheme described in
+ref \cite{oldziej_2004}.
+
+\item{DELTA} (0.01) -- one dimension bin size of the histogram in q.
+
+\item{DELTRMS} (0.05) -- rms dimension bin size in rms-radius of gyration histograms.
+
+\item{DELTRGY} (0.05) - radius of gyration bin size in rms-radius of gyration histograms.
+
+\item{NQ} (1) -- number of q's (can be for entire molecule, fragments, and pairs of fragments).
+
+\item{CXFILE} -- produce the compressed coordinate file with information necessary to compute the probabilities of conformations at any temperature.
+
+\item{HISTOUT} -- if present, the histograms of q at MREMD temperatures are constructed and printed to main output file.
+
+\item{HISTFILE} -- if present, the histograms are also printed to separate files.
+
+\item{ENTFILE} -- if present, histogram of density of states (entropy) is constructed and printed.
+
+\item{RMSRGYMAP} -- if present, 2D histograms of radius of rmsd and radius of gyration at MREMD temperatures are constructed and printed.
+
+\item{WITH\_DIHED\_CONSTR} -- if present, dihedral-angle restraints were imposed in the processed MREMD simulations.
+
+\item{RESCALE} (1) -- Choice of the type of temperature dependence of the force field.
+
+\begin{description}
+
+\item{$>0$} -- no temperature dependence.
+
+\item{1} -- homographic dependence (not implemented yet with any force field).
+
+\item{2} -- hyperbolic tangent dependence \cite{liwo_2007}.
+
+\end{description}
+
+\end{description}
+
+\subsubsection{Molecule data}
+\label{sect:inoutfiles:main:molecule}
+
+\paragraph{General information}
+\label{sect:inoutfiles:main:molecule:geninfo}
+
+\begin{description}
+
+\item{SCAL14} (0.4) -- scale factor of backbone-electrostatic 1,4-interactions.
+
+\item{SCALSCP} (1.0) -- scale factor of SC-p interactions.
+
+\item{CUTOFF} (7.0) -- cut-off on backbone-electrostatic interactions to compute 4- and higher-order correlations.
+
+\item{DELT\_CORR} (0.5) -- thickness of the distance range in which the energy is decreased to zero.
+
+\item{ONE\_LETTER} -- if present, the sequence is to be read in 1-letter code, otherwise 3-letter code.
+
+\end{description}
+
+\paragraph{Sequence information \\ \\}
+\label{sect:inoutfiles:main:molecule:sequence}
+
+
+1st record (keyword-based input):
+
+NRES -- number of residues, including the UNRES dummy terminal residues, if present
+
+Next records: amino-acid sequence
+
+3-letter code: Sequence is input in format 20(1X,A3)
+
+1-letter code: Sequence is input in format 80A1
+
+\paragraph{Dihedral angle restraint information \\ \\}
+\label{sect:inoutfiles:main:molecule:restraints}
+
+
+This is the information about dihedral-angle restraints, if any are present.
+It is specified only when WITH\_DIHED\_CONSTR is present in the first record.
+
+1st line: ndih\_constr -- number of restraints (free format).
+
+2nd line: ftors -- force constant (free format).
+
+Each of the following ndih\_constr lines:
+
+idih\_constr(i),phi0(i),drange(i) (free format)
+
+\begin{description}
+
+\item{idih\_constr(i)} -- the number of the dihedral angle gamma corresponding to the ith restraint.
+
+\item{phi0(i)} -- center of dihedral-angle restraint.
+
+\item{drange(i)} -- range of flat well (no restraints for phi0(i) +/- drange(i)).
+
+\end{description}
+
+\paragraph{Disulfide-bridge data\\ \\}
+\label{sect:inoutfiles:main:molecule:disulfide}
+
+
+1st line: NS, (ISS(I),I=1,NS) (free format)
+
+\begin{description}
+
+\item{NS} -- number of cystine residues forming disulfide bridges.
+
+\item{ISS(I)} -- the number of the Ith disulfide-bonding cystine in the sequence.
+
+\end{description}
+
+nd line: NSS, (IHPB(I),JHPB(I),I=1,NSS) (free format)
+
+\begin{description}
+
+\item{NSS} -- number of disulfide bridges
+
+\item{IHPB(I),JHPB(I)} - the first and the second residue of ith disulfide link
+
+\end{description}
+
+Because the input is in free format, each line can be split.
+
+\subsubsection{Energy-term weights and parameter files}
+\label{sect:inoutfiles:main:weights}
+
+There are NPARMSET records specified below.
+All items described in this section are input in keyword-based mode.
+
+1st record: Weights for the following energy terms:
+
+\begin{description}
+
+\item{WSC} (1.0) -- side-chain-side-chain interaction energy.
+\item{WSCP} (1.0) -- side chain-peptide group interaction energy.
+\item{WELEC} (1.0) -- peptide-group-peptide group interaction energy.
+\item{WEL\_LOC (1.0)} -- third-order backbone-local correlation energy.
+\item{WCORR} (1.0) -- fourth-order backbone-local correlation energy.
+\item{WCORR5} (1.0) -- fifth-order backbone-local correlation energy.
+\item{WCORR6} (1.0) -- sixth-order backbone-local correlation energy.
+\item{WTURN3} (1.0) -- third-order backbone-local correlation energy of pairs of peptide groups separated by a single peptide group.
+\item{WTURN4} (1.0) -- fourth-order backbone-local correlation energy of pairs of peptide groups separated by two peptide groups.
+\item{WTURN6} (1.0) -- sixth-order backbone-local correlation energy for pairs of peptide groups separated by four peptide groups.
+\item{WBOND} (1.0) -- virtual-bond-stretching energy.
+\item{WANG} (1.0) -- virtual-bond-angle-bending energy.
+\item{WTOR} (1.0) -- virtual-bond-torsional energy.
+\item{WTORD} (1.0) -- virtual-bond-double-torsional energy.
+\item{WSCCOR} (1.0) -- sequence-specific virtual-bond-torsional energy.
+\item{WDIHC} (0.0) -- dihedral-angle-restraint energy.
+\item{WHPB} (1.0) -- distance-restraint energy.
+
+\end{description}
+
+2nd record: Parameter files. If filename is not specified that corresponds to particular parameters, the respective name from the C-shell script will be assigned. If no files are to be specified, an empty line must be inserted.
+
+\begin{description}
+\item{BONDPAR} -- bond-stretching parameters.
+\item{THETPAR} -- backbone virtual-bond-angle-bending parameters.
+\item{ROTPAR} -- side-chain-rotamer parameters.
+\item{TORPAR} -- backbone-torsional parameters.
+\item{TORDPAR} -- backbone-double-torsional parameters.
+\item{FOURIER} -- backbone-local -- backbone-electrostatic correlation parameters.
+\item{SCCORAR} -- sequence-specific backbone-torsional parameters (not used at present).
+\item{SIDEPAR} -- side-chain-side-chain-interaction parameters.
+\item{ELEPAR} -- backbone-electrostatic-interaction parameters.
+\item{SCPPAR} -- backbone-side-chain-interaction parameters.
+\end{description}
+
+\subsubsection{(M)REMD/Hamiltonian (M)REMD setting specification}
+\label{sect:inoutfiles:main:MREMD}
+
+If HAMIL\_REP is present in general data, read the following group of records only once; otherwise, read for each parameter set (NPARSET times total).
+
+\begin{description}
+
+\item{NT} (1) -- number of temperatures.
+
+\item{REPLICA} -- if present, replicas in temperatures were specified with this parameter set.
+
+\item{UMBRELLA} -- if present, umbrella-sampling was run with this parameter set.
+
+\item{READ\_ISET} -- if present, umbrella-sampling-window number is read from the compressed Cartesian coordinate (cx) file even if the data are not from umbrella-sampling run(s). ISET is present in the cx files from the present version of UNRES.
+
+\end{description}
+
+Following NT records are for consecutive temperature replicas; each record is
+organized as keyword-based input:
+
+\begin{description}
+
+\item{TEMP} (298.0) - initial temperature of this replica (replicas in MREMD).
+
+\item{FI} (0.0) - initial values of the dimensionless free energies for all q-restraint windows for this replica (NR values).
+
+\item{KH} (100.0) - force constants of q restraints (NR values).
+Q0 (0.0d0) - q-restraint centers (NR values)</p>
+
+\end{description}
+
+\subsubsection{Information of files from which to read conformations}
+\label{sect:inoutfile:main:conffiles}
+
+If HAMIL\_REP is present in general data, read the following two records only once; otherwise, read for each parameter set (NPARSET times total).
+
+1st record (keyword-based input):.
+
+For temperature replica only ONE record is read; for non-(M)REMD runs, NT records must be supplied. The records are in keyword-based format.
+
+\begin{description}
+\item{NFILE\_ASC} -- number of files in ASCII format (UNRES Cartesian coordinate (x) files) for current parameter set.
+
+\item{NFILE\_CX} -- number of compressed coordinate files (cx files) for current parameter set.
+
+\item{NFILE\_BINi} -- number of binary coordinate files (now obsolete because it requires initial conversion of ASCII format trajectories into binary format).
+
+\end{description}
+
+It is strongly recommended to use cx files from (M)REMD runs with TRAJ1FILE option. Multitude of trajectory files which are opened and closed by different processors might impair file system accessibility. Should you wish to process trajectories each one of which is stored in a separate file, better collate the required slices of them first to an x file by using the xdrf2x program piped to the UNIX cat command.
+
+coordinate file name(s) without extension.
+
+\subsubsection{Information of reference structure and comparing scheme}
+\label{sect:inoutfile:main:reference}
+
+The following records pertain to setting up the classification of conformation aimed ultimately at obtaining a class numbers. Fragments and pairs of fragments are specified and compared against those of reference structure in terms of secondary structure, number of contacts, rmsd, virtual-bond-valence and dihedral angles, etc. Then the class number is constructed as described in ref 3. A brief description of comparison procedure is as follows:
+
+\begin{enumerate}
+
+\item
+Elementary fragments usually corresponding to elements of secondary or supersecondary structure are selected. Based on division into fragments, levels of structural hierarchy are defined.
+
+\item
+At level 1, each fragment is checked for agreement with the corresponding fragment in the native structure. Comparison is carried out at two levels: the secondary structure agreement and the contact-pattern agreement level.
+
+At the secondary structure level the secondary structure (helix, strand or undefined) in the fragment is compared with that in the native fragment in a residue-wise manner. Score 0 is assigned if the structure is different in more than 1/3 of the fragment, 1 is assigned otherwise.
+
+The contact-pattern agreement level compares the contacts between the peptide groups of the backbone of the fragment and the native fragment and also compares their virtual-bond dihedral angles gamma. It is allowed to shift the sequence by up to 3 residues to obtain contact pattern match. A score of 0 is assigned if more than 1/3 of native contacts do not occur or there is more than 60 deg (usually, but this cutoff can be changed) maximum difference in gamma. Otherwise score 1 is assigned.
+
+The total score of a fragment is an octal number consisting of bits hereafter referred to S (secondary structure) C (contact match) and H (sHift) (they are in the order HCS). Their values are as follows:
+
+\begin{description}
+\item{S} -- 1 native secondary structure; 0 otherwise,
+\item{C} -- 1 native contact pattern; 0 otherwise,
+\item{H} -- 1 contact match obtained without sequence shift 0 otherwise.
+\end{description}
+
+For example,
+octal 7 (111) corresponds to native secondary structure, native contact pattern, and no need to shift the sequence for contact match;
+octal 1 (001) corresponds to native secondary structure only (i.e., nonnative contact pattern).
+
+\item
+At level 2, contacts between (i) the peptide groups or (ii) the side chains within pairs of fragments are compared. Case (i) holds when we seek contacts between the strands of a larger beta-sheet formed by two fragments, case (ii) when we seek the interhelix or helix-beta sheet contacts. Additionally, the pairs of fragments are compared with their native counterparts by rmsd.
+
+Score 0 is assigned to a pair of fragments, if it has less than 2/3 native contacts and too large rmsd (a cut-off of 0.1 A/residue is set), score 1 if it has enough native contacts and sufficiently low rmsd, but the sequence has to be shifted to obtain a match, and score 2, if sufficient match is obtained without shift.
+
+\item
+At level 3 and higher, triads, quadruplets,..., etc. of fragments are compared in terms of rmsd from their native counterparts (the last level corresponds to comparing whole molecules). The score (0, 1, or 2) is assigned to each composite fragment as in the case of level 2.
+
+\item
+The TOTAL class number of a structure is a binary number composed of parts of scores of fragments, fragment pairs, etc. It is illustrated on the following example; it is assumed that the molecule has three fragment as in the case of 1igd.
+
+\end{enumerate}
+
+\begin{verbatim}
+level 1 level 2 level 3
+123 123 123||1-2 1-3 2-3 1-2 1-3 2-3 || 1-2-3 | 1-2-3 ||
+sss|ccc|hhh|| c c c | h h h || r | h ||
+\end{verbatim}
+
+Bits s, c, and h of level 1 are explained in point 2; bits c and h of level 2 pertain to contact-pattern match and shift; bits r and h of level 3 pertain to rmsd match and shift for level 3.
+
+The input is specified as follows:
+
+1st record (keyword-based input):
+
+\begin{description}
+
+\item{VERBOSE} -- if present, detailed output in classification (use if you want to fill up the disk).
+
+\item{PDBREF} -- if present, the reference structure is read from the pdb.
+
+\item{BINARY} -- if present, the class will be output in octal/quaternary/binary format for levels 1, 2, and 3, respectively.
+
+\item{DONT\_MERGE\_HELICES} -- if present, the pieces of helices that contain only small breaks of hydrogen-bonding contacts (e.g., a kink) are not merged in a larger helix.
+
+\item{NLEVEL=n} -- number of classification levels.
+
+\item{n$>$0} -- the fragments for n levels will be defined manually.
+
+\item{n$<$0} -- the number of levels is -n and the fragments will be detected automatically.
+
+\item{START=n} -- the number of conformation at which to start.
+
+\item{END=n} -- the number of conformation at which to end.
+
+\item{FREQ=n} (1) - sampling frequency of conformations; e.g. FREQ=2 means that every second conformation will be considered.
+
+\item{CUTOFF\_UP=x} - upper boundary of rmsd cutoff (the value is per 50 residues).
+
+\item{CUTOFF\_LOW=x} -- lower boundary of rmsd cutoff (per 50 residues).
+
+\item{RMSUP\_LIM=x} -- lower absolute boundary of rmsd cutoff (regardless of fragment length).
+
+\item{RMSUPUP\_LIM=x} -- upper absolute boundary of rmsd cutoff (regardless of fragment length).
+
+\item{FRAC\_SEC=x} (0.66666) the fraction of native secondary structure to consider a fragment native in secondary structure.
+
+\end{description}
+
+2nd record:
+
+For nlevel$<$0 (automatic fragment assignment):
+
+\begin{description}
+
+\item{SPLIT\_BET=n} (0) : if 1, the hairpins are split into strands and strands are considered elementary fragment.
+
+\item{ANGCUT\_HEL=x} (50): cutoff on gamma angle differences from the native for a helical fragment.
+
+MAXANG\_HEL=x (60) : as above but maximum cutoff
+
+\item{ANGCUT\_BET=x} (90), MAXANG\_BET=x (360), ANGCUT\_STRAND=x (90), MAXANG\_STRAND=x (360) -- same but for a hairpin or sheet fragment.
+
+\item{FRAC\_MIN=x} (0.6666) -- minimum fraction of native secondary structure.
+
+\item{NC\_FRAC\_HEL=x (0.5)} -- fraction of native contacts for a helical fragment.
+
+\item{NC\_REQ\_HEL=x} (0) -- minimum required number of contacts.
+
+\item{NC\_FRAC\_BET=x} (0.5), NC\_REQ\_BET=x (0) -- same for beta sheet fragments.
+
+\item{NC\_FRAC\_PAIR=x} (0.3), NC\_REQ\_PAIR=x (0) : same for pairs of segments.
+
+\item{NSHIFT\_HEL=n} (3), NSHIFT\_BET=n (3), NSHIFT\_STRAND=n (3), NSHIFT\_PAIR=n (3) -- allowed sequence shift to match native and compared structure for the respective types of secondary structure.
+
+\item{RMS\_SINGLE=n} (0), CONT\_SINGLE=n (1), LOCAL\_SINGLE=n (1), RMS\_PAIR=n (0).
+
+\item{CONT\_PAIR=n} (1) -- types of criteria in considering the geometry of a fragment or pair native; 1 means that the criterion is turned on.
+
+\end{description}
+
+For nlevel$>$0 (manual assignment):
+
+Level 1:
+
+1st line:
+
+\begin{description}
+
+\item{NFRAG=n} -- number of elementary fragments.
+
+\end{description}
+
+Next lines (one group of lines per each fragment):
+
+1st line:
+
+\begin{description}
+
+\item{NPIECE=n} -- number of segments constituting the fragment.
+
+\item{ANGCUT}, MAXANG, FRAC\_MIN, NC\_FRAC, NC\_REQ -- criterial numbers of native-likeness as for automatic classification.
+
+\item{LOCAL}, ELCONT, SCCONT, RMS : types of criteria implemented, as for automatic classification except that ELECONT and SCCONT mean that electrostatic or side-chain contacts are considered, respectively.
+
+\end{description}
+
+NPIECE following lines:
+
+IFRAG1=n, IFRAG2=n -- the start and end residue of a continuous segment constituting a fragment.
+
+Level 2 and higher:
+
+1st line:
+
+\begin{description}
+
+\item{NFRAG=n} -- number of fragments considered at this level.
+
+\end{description}
+
+For each fragment the following line is read:
+
+\begin{description}
+
+\item{NPIECE=n} -- number of elementary fragments (as defined at level 1) constituting this composite fragment.
+
+\item{IPIECE=i1 i2 ... in} -- the numbers of these fragments.
+
+\item{NC\_FRAC}, NC\_REQ : contact criteria (valid only for level 2).
+
+\item{ELCONT}, SCCONT, RMS : as for level 1; note, that for level 3 and higher the only criterion of nativelikeness is rms.
+
+\end{description}
+
+3rd (for nlevel$<$0) or following (for n$>$0) line:
+
+Name of the file with reference structure (e.g., the pdb file with the experimental structure)
+
+\subsection{The structure of the main output file (out)}
+\label{sect:inoutfiles:output:main}
+
+The initial portion of the main output file, named INPUT.out\_POT\_000 contains information of parameter files specified in the C-shell script, compilation info, and the UNRES numeric code of the amino-acid sequence.
+Subsequently, actual energy-term weights and parameter files are printed. If lprint was set at .true. in parmread.F, all energy-function parameters are printed. If REFSTR was specified in the control-data list, the program then outputs the read reference-structure coordinates and partition of structure into fragments.
+Subsequently, the information about the number of structures read in and those that were rejected is printed followed by succinct information form the iteration process. Finally, the histograms (also output separately to specific histogram files; see section 6.6) and the data of the dependence of free energy, energy, heat capacity, and conformational averages on temperature are printed (these are also output separately to file described in section \ref{sect:inoutfiles:histograms}).
+
+The output files corresponding to non-master processors (INPUT.out\_POT\_xxx where xxx$>$0 contain only the information up to the iteration protocol. These files can be deleted right after the run.
+
+\subsection{The thermodynamic quantity and ensemble average (thermal) files}
+\label{sect:inoutfiles:outpput:thermo}
+
+The files INPUT.thermal or INPUT\_slice\_yy.thermal contain thermodynamic, ensemble-averaged conformation-dependent quantities and their temperature derivatives. The structure of a record is as follows:
+
+\begin{tabular}{p{2cm}p{2cm}p{2cm}p{2cm}p{2cm}p{2cm}p{2cm}}
+ T& F& E& $q_1...q_n$& rmsd& Rgy& Cv\\
+ 298.0& -83.91454& -305.28112& 0.30647& 6.28347& 11.61204&0.70886E+01\\
+\end{tabular}
+
+\begin{tabular}{p{2.5cm}p{2.5cm}p{2.5cm}p{2.5cm}p{2.5cm}p{2.5cm}}
+ $var(q_1) ...$ & var(rmsd)& var(Rgy)& $cov(q_1,E) ...$ & cov(rmsd,E)& cov(Rgy,E)\\
+ $var(q_n)$& & & $cov(q_n,E)$& & \\
+ 0.35393E-02& 0.51539E+01& 0.57012E+00& 0.43802E+00& 0.62384E+01& 0.33912E+01\\
+\end{tabular}
+
+where:
+
+\begin{description}
+
+\item{T} -- absolute temperature (in K),
+
+\item{F} -- free energy at T,
+
+\item{E} -- average energy at T,
+
+\item{$q_1..q_n$}: ensemble-averaged q values at T (usually only the total q corresponding to whole molecule is requested, as in the example above, but the user can specify more than one fragment or pair of fragments for which the q's are calculated, If there is no reference structure, this entry contains a 0,
+
+\item{rmsd} -- ensemble-averaged root mean square deviation at T,
+
+\item{Rgy} -- ensemble-averaged radius of gyration computed from Calpha coordinates at T,
+
+\item{$C_v$} -- heat capacity at T,
+
+\item{$var(q_1)...var(q_n)$} -- variances of q's at T,
+
+\item{var(rmsd)} -- variance of rmsd at T,
+
+\item{var(Rgy)} -- variance of radius of gyration at T,
+
+\item{$cov(q_1,E)...cov(q_n,E)$} -- covariances of q's and energy at T,
+
+\item{cov(rmsd,E)} -- covariance of rmsd and energy at T,
+
+\item{cov(Rgy,E)} -- covariance of radius of gyration and energy at T.
+
+\end{description}
+
+According to Camacho and Thirumalali (Europhys. Lett., 35, 627, 1996), the maximum of the variance of the radius of gyration corresponds to the collapse point of a polypeptide chain and the maximum variance of q or rmsd corresponds to the midpoint of the transition to the native structure. More precisely, these points are inflection points in the plots of the respective quantities which, with temperature-independent force field, are proportional to their covariances with energy.
+
+\subsection{The conformation summary with classification (stat) files}
+\label{sect:inoutfiles:class}
+
+The stat files (with names INPUT\_POT\_xxx.stat or INPUT\_POT\_sliceyyxxx.stat; where yy is the number of a slice and xxx is the rank of a processor) contain the output of the classification of subsequent conformations (equally partitioned between processors). The files can be concatenated by processor rank to get a summary file. Each line has the following structure (example values are also provided):
+
+
+\begin{tabular}{|c|cccc|}\hline
+&&\multicolumn{3}{c|}{whole molecule}\\
+\cline{2-5}
+No&energy&rmsd&q&ang\\ \hline
+ 9999& -122.42& 4.285&0.3751& 47.8\\ \hline
+\end{tabular}
+
+\begin{tabular}{|cccccccccccc|c|}\hline
+\multicolumn{13}{|c|}{level 1}\\ \hline
+\multicolumn{6}{|c}{frag 1}&\multicolumn{3}{c}{frag 2}&\multicolumn{3}{c|}{frag 3}&class 1\\ \cline{1-12}
+n1&n2&n3&rmsd&q&ang&rmsd&q&ang&rmsd&q&ang&\\ \hline
+ 4&10&21 & 0.6&0.33& 16.7& 3.6&0.42& 56.3& 0.7&0.12& 16.5&737 \\ \hline
+\end{tabular}
+
+\begin{tabular}{|cccccc|c|cc|c|c|} \hline
+\multicolumn{7}{|c|}{level 2}&\multicolumn{3}{c|}{level 3}&\\
+\cline{1-10}
+nc1&nc2&rmsd&q&rmsd&q&class 2&rmsd&q&class 3&class\\ \hline
+9& 0& 1.6&0.20& 4.3&0.20&20& 0& 4.0&2&737.20.2\\ \hline
+\end{tabular}
+
+% | level 1 | level 2 | level3 |
+% | | | |
+% whole mol | frag1 frag2 frag3 cl1 | | |
+%No energy rmsd q ang dif|n1n2 n3 rms q ang rms q ang rms q ang | nc1nc2 rms q rms q cl2| rms cl3|class
+% 9999 -122.42 4.285 0.3751 47.8 |4 10 21 0.6 0.33 16.7 3.6 0.42 56.3 0.7 0.12 16.5 737 | 9 0 1.6 0.20 4.3 0.20 20 | 0 4.0 2 |737.20.2
+
+where
+
+\begin{description}
+
+\item{No} -- the number of the conformation.
+
+\item{``whole molecule''} denotes the characteristics of the whole molecule q = 1-Wolynes'q.
+
+\item{level 1, 2, and 3} denote the characteristics computed for the respective fragments as these levels.
+
+\item{n1, n2, n3} -- number of native contacts for a given segment.
+
+\item{cl1, cl2, cl3} -- group of segment classes for segments at level 1, 2, and 3, respectively.
+
+\item{class} -- total class of the conformation.
+
+\end{description}
+
+The octal/quaternary/binary numbers denoting the class for a fragment at level 1, 2, and 3, respectively, are described in ref. \cite{oldziej_2004}.
+
+\subsection{The histogram files}
+\label{sect:inoutfiles:histograms}
+
+The histogram file with names INPUT\_[par\_yy][\_slice\_xx].hist where xx denotes the number of the slice and yy denotes the number of the parameter if SEPARATE\_PARSET was specified in input contain histograms of q at replica temperatures and energy-parameter sets; with SEPARATE\_PARSET histograms corresponding to subsequent parameter sets are saved in files with par\_yy infixes. The histograms are multidimensional if q is a vector (usually, however, q corresponds to the entire molecule and, consequently, the histograms are one-dimensional). The histogram files are printed if histfile and histout was specified in the control data record.
+
+Each line of a histogram file corresponds to a given (multidimensional) bin in q contains the following:
+
+
+\begin{itemize}
+
+\item
+$q_1,...,q_n$ at a given bin (format f6.3 for each)
+
+\item
+histogram values for subsequent replica temperatures (format e20.10 for each)
+
+\item
+iparm (the number of parameter set; format i5)
+
+\item
+If SEPARATE\_PARSET was not specified, the entries corresponding to each parameter follow one another.
+
+\end{itemize}
+
+The state density is printed to file(s) INPUT[\_slice\_xx].ent. Each line contains the left boundary of the energy bin and ln(state density) followed by ``ent'' string. At present, the state density is calculated correctly only if one energy-parameter set is used.</p>
+
+\subsection{The rmsd-radius of gyration potential of mean force files}
+\label{sect:inoutfiles:rmsd-rgy}
+
+These files with names INPUT[\_par\_yy][\_slice\_xx].rmsrgy contain the two-dimensional potentials of mean force in rmsd and radius of gyration at all replica-exchange temperatures and for all energy-parameter sets.
+A line contains the left boundaries of the radius of gyration -- rmsd bin (radius of gyration first) (format 2f8.2) and the PMF values at all replica-exchange temperatures (e14.5), followed by the number of the parameter set.
+With SEPARATE\_PARSET, the PMFs corresponding to different parameter sets are printed to separate files.
+
+\subsection{The PDB files}
+\label{sect:inoutfiles:PDB}
+
+The PDB files with names INPUT\_[slice\_xx\_]Tyyy.pdb, where Tyyy specifies a given replica temperature contain the conformations whose probabilities at replica temperature T sum to 0.99, after sorting the conformations
+by probabilities in descending order. The PDB files follow the standard format; see \href{ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf}{\textcolor{blue}{ftp://ftp.wwpdb.org/pub/pdb/doc/format\_descriptions}}.
+%/Format_v33_Letter.pdf">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf</a>.
+For single-chain proteins, an example is as follows:
+
+\begin{verbatim}
+REMARK CONF 9059 TEMPERATURE 330.0 RMS 8.86
+REMARK DIMENSIONLESS FREE ENERGY -1.12726E+02
+REMARK ENERGY -2.22574E+01 ENTROPY -7.87818E+01
+ATOM 1 CA VAL 1 8.480 5.714 -34.044
+ATOM 2 CB VAL 1 9.803 5.201 -33.968
+ATOM 3 CA ASP 2 8.284 2.028 -34.925
+ATOM 4 CB ASP 2 7.460 0.983 -33.832
+.
+.
+.
+ATOM 115 CA LYS 58 28.446 -3.448 -12.936
+ATOM 116 CB LYS 58 26.613 -4.175 -14.514
+TER
+CONECT 1 3 2
+.
+.
+.
+CONECT 113 115 114
+CONECT 115 116
+\end{verbatim}
+
+where
+
+\begin{description}
+
+\item{CONF} is the number of the conformation from the processed slice of MREMD trajectories.
+
+\item{TEMPERATURE} is the replica temperature.
+
+\item{RMS} is the Calpha rmsd from the reference (experimental) structure.
+
+\item{DIMENSIONLESS FREE ENERGY} is -log(probability) (equation 14 of ref 2) for the conformation at this replica temperature calculated by WHAM.
+
+\item{ENERGY} is the UNRES energy of the conformation at the replica temperature (note that UNRES energy is in general temperature dependent).
+
+\item{ENTROPY} is the omega of equation 15 of ref 2 of the conformation.
+
+\end{description}
+
+In the ATOM entries, CA denotes a Calpha atom and CB denotes UNRES side-chain atom. The CONECT entries specify the C$^\alpha_i\cdots$C$^\alpha_{i-1}$, C$^\alpha_i\cdots$C$^\alpha_{i+1}$ and C$^\alpha_i\cdots$SC$_i$ links.
+
+The PDB files generated for oligomeric proteins are similar except that chains are separated with TER and molecules with ENDMDL records and chain identifiers are included. An example is as follows:
+
+\begin{verbatim}
+REMARK CONF 765 TEMPERATURE 301.0 RMS 11.89
+REMARK DIMENSIONLESS FREE ENERGY -4.48514E+02
+REMARK ENERGY -3.58633E+02 ENTROPY 1.51120E+02
+ATOM 1 CA GLY A 1 -0.736 11.305 24.600
+ATOM 2 CA TYR A 2 -3.184 9.928 21.998
+ATOM 3 CB TYR A 2 -1.474 10.815 20.433
+.
+.
+.
+ATOM 40 CB MET A 21 -4.033 -2.913 27.189
+ATOM 41 CA GLY A 22 -5.795 -10.240 27.249
+TER
+ATOM 42 CA GLY B 1 6.750 -6.905 19.263
+ATOM 43 CA TYR B 2 5.667 -4.681 16.362
+.
+.
+.
+ATOM 163 CB MET D 21 4.439 12.326 -4.950
+ATOM 164 CA GLY D 22 10.096 14.370 -9.301
+TER
+CONECT 1 2
+CONECT 2 4 3
+.
+.
+.
+CONECT 39 41 40
+CONECT 42 43
+.
+.
+.
+CONECT 162 164 163
+ENDMDL
+\end{verbatim}
+
+\subsection{The compressed Cartesian coordinates (cx) files}
+\label{sect:inoutfiles:cx}
+
+These files contain compressed data in the Europort Data Compression XDRF library format written by Dr. F. van Hoesel, Groeningen University (\href{http://hpcv100.rc.rug.nl/xdrfman.html}{http://hpcv100.rc.rug.nl/xdrfman.html}.
+The files are written by the cxwrite subroutine. The resulting cx file contains the omega factors to compute probabilities of conformations at any temperature and any energy-function parameters if Hamiltonian replica
+exchange was performed in the preceding UNRES run. The files have general names INPUT[\_par\_yy][\_slice\_xx].cx where xx is slice number and yy is parameter-set.
+
+The items written to the cx file are as follows (the precision is 5 significant digits):
+
+\begin{enumerate}
+\item
+Cartesian coordinates of Calpha and SC sites</p>
+\item
+nss (number of disulfide bonds)
+\item
+if nss$>$0:
+\begin{enumerate}
+\item
+ihpb (first residue of a disulfide link)
+\item
+jhpb (second residue of a disulfide link)
+\item
+UNRES energy at that replica temperature that the conformation was at snapshot-recording time,
+\item
+ln(omega) of eq 15 of ref \cite{liwo_2007},
+\end{enumerate}
+\item
+C$^\alpha$ rmsd
+\item
+conformation class number (0 if CLASSIFY was not specified).
+\end{enumerate}
+
+\newpage
+
+\section{SUPPORT}
+\label{sect:support}
+
+ Dr. Adam Liwo\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
+ phone: +48 58 523 5430\\
+ fax: +48 58 523 5472\\
+ e-mail: \href{mailto:adam@chem.univ.gda.pl}{\textcolor{blue}{adam@chem.univ.gda.pl}}\\
+
+ Dr. Cezary Czaplewski\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
+ phone: +48 58 523 5430\\
+ fax: +48 58 523 5472\\
+ e-mail: \href{mailto:czarek@chem.univ.gda.pl}{\textcolor{blue}{czarek@chem.univ.gda.pl}}\\
+\\
+
+ Adam Sieradzan\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Sobieskiego 18, 80-952 Gdansk Poland.\\
+ phone: +48 58 523 5430\\
+ fax: +48 58 523 5472\\
+ e-mail: \href{mailto:adasko@chem.univ.gda.pl}{\textcolor{blue}{adasko@chem.univ.gda.pl}}\\
+
+Prepared by Adam Liwo, 02/19/12.
+
+\LaTeX version, 09/27/12.
+
+\end{document}
--- /dev/null
+\documentclass[12pt]{article}
+%\usepackage{latex2html}
+\usepackage{enumerate}
+\usepackage{longtable}
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{color}
+\parindent=0pt
+\parskip=12pt
+\textheight=24cm
+\textwidth=18cm
+\topmargin=-2.5cm
+\oddsidemargin=-0.5cm
+\setcounter{secnumdepth}{5}
+\setcounter{tocdepth}{5}
+\begin{document}
+\sloppy
+
+\title{CLUSTER\\
+Cluster analysis of UNRES simulation results}
+
+\author{Laboratory of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Wita Stwosza 63\\ 80-308 Gdansk, Poland\\
+\\
+\\
+Scheraga Group\\ Baker Laboratory of Chemistry \\
+and Chemical Biology\\ Cornell University\\ Ithaca, NY 14853-1301, USA}
+
+\maketitle
+
+\newpage
+
+\tableofcontents
+
+% 1. License terms
+% 2. References
+% 3. Functions of the program
+% 4. Installation
+% 5. Running the program
+% 6. Input and output files
+% 6.1. Summary of files
+% 6.2. The main input file
+% 6.2.1. Title
+% 6.2.2. General data
+% 6.2.3. Energy-term weights and parameter files
+% 6.2.4 Molecule data
+% 6.2.4.1. Sequence information
+% 6.2.4.2. Dihedral angle restraint information
+% 6.2.4.3. Disulfide-bridge data
+% 6.2.5. Reference structure
+% 6.3. Main output file (out)
+% 6.4. Output coordinate files
+% 6.4.1. The internal coordinate (int) files
+% 6.4.2. The Cartesian coordinate (x) files
+% 6.4.3. The PDB files
+% 6.4.3.1. CLUST-UNRES runs
+% 6.4.3.2. CLUST-WHAM runs
+% 6.4.3.2.1. Conformation family files
+% 6.4.3.2.2. Average-structure file
+% 6.5. The conformation-distance file
+% 6.6. The clustering-tree PicTeX file
+% 7. Support
+
+\newpage
+
+\section{LICENSE TERMS}
+\label{sect:license}
+
+\begin{itemize}
+
+\item
+ This software is provided free of charge to academic users, subject to the condition that no part of it be sold or used otherwise for commercial purposes, including, but not limited to its incorporation into commercial software packages, without written consent from the authors. For permission contact Prof. H. A. Scheraga, Cornell University.
+
+\item
+ This software package is provided on an ``as is'' basis. We in no way warrant either this software or results it may produce.
+
+\item
+ Reports or publications using this software package must contain an acknowledgment to the authors and the NIH Resource in the form commonly used in academic research.
+
+\end{itemize}
+
+\newpage
+
+\section{REFERENCES}
+\label{sect:references}
+
+The program incorporates the hierarchical-clustering subroutine, hc.f written
+by G. Murtagh (refs 1 and 2). The subroutine contains seven methods of
+hierarchical clustering.
+
+\begingroup
+\renewcommand{\section}[2]{}%
+\begin{thebibliography}{10}
+
+\bibitem{murtagh_1985}
+Murtagh. Multidimensional clustering algorithms; Physica-Verlag:
+Vienna, Austria, 1985.
+
+\bibitem{murtagh_1987}
+F. Murtagh, A. Heck. MultiVariate data analysis; Kluwer Academic:
+Dordrecht, Holland, 1987.
+
+\bibitem{liwo_2007}
+A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, K. Wachucik,
+H.A. Scheraga.
+Modification and optimization of the united-residue (UNRES) potential
+energy function for canonical simulations. I. Temperature dependence of the
+effective energy function and tests of the optimization method with single
+training proteins. {\it J. Phys. Chem. B}, {\bf 2007}, 111, 260-285.
+
+\bibitem{oldziej_2004}
+S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+Optimization of the UNRES force field by hierarchical design of the
+potential-energy landscape. 2. Off-lattice tests of the method with single
+proteins. {\it J. Phys. Chem. B.}, {\bf 2004}, 108, 16934-16949.
+
+\end{thebibliography}
+\endgroup
+
+\newpage
+
+\section{FUNCTIONS OF THE PROGRAM}
+\label{sect:functions}
+
+The program runs cluster analysis of UNRES simulation results. There are two
+versions of the program depending on the origin of input conformation:
+
+\begin{enumerate}
+
+\item
+ CLUST-UNRES: performs cluster analysis of conformations that are obtained
+ directly from UNRES runs (CSA, MCM, MD, (M)REMD, multiple-conformation
+ energy minimization). The source code and other important files are
+ deposited in CLUST-UNRES subdirectory
+
+ The source code of this version is deposited in clust-unres/src
+
+\item
+ CLUST-WHAM: performs cluster analysis of conformations obtained in UNRES
+ MREMD simulations and then processed with WHAM (weighted histogram analysis
+ method). This enables the user to obtain clusters as conformational
+ ensembles at a given temperature and to compute their probabilities
+ (section 2.5 of ref 3). This version is deposited in the CLUST-WHAM
+ subdirectory. This version has single- and multichain variants, whose
+ source codes are deposited in the following subdirectories:
+
+\begin{enumerate}
+
+\item
+ clust-wham/src single-chain proteins
+
+\item
+ clust-wham/src-M oligomeric proteins
+
+\end{enumerate}
+
+\end{enumerate}
+
+The version developed for oligomeric proteins treats whole system as a single
+chain with dummy residues inserted. It also works for single chains but is
+not fully checked and it is recommended to use single-chain version for
+single-chain proteins.
+
+\section{INSTALLATION}
+\label{sect:install}
+
+It is recommended to use Cmake to install the whole package; please see
+Installation Guide.
+
+Customize Makefile to your system. See section 7 of the description of UNRES
+for compiler flags that are used to created executables for a particular
+force field. There are already several Makefiles prepared for various
+systems and force fields.
+
+Run make in the appropriate source directory version. CLUST-UNRES runs
+only in single-processor mode an CLUST-WHAM runs in both serial and parallel
+mode [only conformation-distance (rmsd) calculations are parallelized].
+The parallel version uses MPI.
+
+\section{RUNNING THE PROGRAM}
+\label{sect:running}
+
+The program requires a parallel system to run. Depending on system,
+either the wham.csh C-shell script (in WHAM/bin directory) can be started
+using mpirun or the binary in the C-shell script must be executed through
+mpirun. See the wham.csh C-shell script and section 6 for the files
+processed by the program.
+
+\newpage
+
+\section{INPUT AND OUTPUT FILES}
+\label{sect:inoutfiles}
+
+\subsection{Summary of files}
+\label{sect:inoutfiles:summary}
+
+The C-shell script wham.csh is used to run the program (see the
+bin/WHAM directory). The data files that the script needs are mostly the same as
+for UNRES (see section 6 of UNRES description). In addition, the environmental
+variable CONTFUN specifies the method to assess whether two side chains
+are at contact; if EONTFUN=GB, the criterion defined by eq 8 of ref 4 is
+used to assess whether two side chains are at contact. Also, the parameter
+files from the C-shell scripts are overridden if the data from Hamiltonian
+MREMD are processed; if so, the parameter files are defined in the main
+input file.
+
+The main input file must have inp extension. If it is INPUT.inp, the output
+files are as follows:
+
+Coordinate input file COORD.ext, where ext denotes file extension in one of the
+following formats:
+
+\begin{description}
+\item{int} (extension int; UNRES angles theta, gamma, alpha, and beta),
+\item{x} (extension x; UNRES Cartesian coordinate format; from MD),
+\item{pdb} (extension pdb; Protein Data Bank format; fro MD),
+\item{cx} (extension cx; xdrf format; from WHAM).
+\end{description}
+
+\begin{description}
+\item{INPUT\_clust.out} (single-processor mode) or INPUT\_clust.out\_xxx (parallel mode) --
+ output file(s) (INPUT.out\_000 is the main output file for parallel mode).
+
+\item{COORD\_clust.int} -- leading (lowest-energy) members of the families.
+ in internal-coordinate format.
+\item{COORD\_clust.x} -- leading members of the families in UNRES Cartesian coordinate
+ format.
+\item{COORD\_xxxx.pdb} or COORD\_xxxx\_yyy.pdb (CLUST-UNRES) -- PDB file of member yyy
+ of family xxxx; yyy is omitted if the family contains only one member
+ within a given energy cut-off.
+\item{COORD\_TxxxK\_yyyy.pdb} -- concatenated conformations in PDB format of the
+ members of family yyyy clustered at T=xxxK ranked by probabilities in
+ descending order at this temperature (CLUST-WHAM).
+\item{COORD\_T\_xxxK\_ave.pdb} -- cluster-averaged coordinates and coordinates of a
+ member of each family that is closest to the cluster average in PDB
+ format, concatenated in a single file (CLUST-WHAM).
+
+\item{INPUT\_clust.tex} -- PicTeX code of the cluster tree.
+
+\item{INPUT.rms} -- rmsds between conformations.
+
+\end{description}
+
+\subsection{Main input file}
+\label{sect:inoutfiles:main}
+
+This file has the same structure as the UNRES input file; most of the data are
+input in a keyword-based form (see section 7.1 of UNRES description). The data
+are grouped into records, referred to as lines. Each record, except for the
+records that are input in non-keyword based form, can be continued by placing
+an ampersand (\&) in column 80. Such a format is referred to as the data list
+format.
+
+In the following description, the default values are given in parentheses.
+
+\subsubsection{Title}
+
+An 80-character string from the first line is input.
+
+\subsubsection{General data}
+\label{sect:inoutfiles:main:general}
+
+(Data list format.)
+
+\begin{description}
+
+\item{NRES} (0) -- the number of residues.
+
+\item{ONE\_LETTER} -- if present, the sequence is input in one-letter code.
+
+\item{SYM} (1) -- number of chains with same sequence (for oligomeric proteins only).
+
+\item{WITH\_DIHED\_CONSTR} -- if present, dihedral-angle restraints were imposed in the
+ processed MREMD simulations
+
+\item{RESCALE} (1) -- Choice of the type of temperature dependence of the force field.
+
+\begin{description}
+\item{0} -- no temperature dependence,
+\item{1} -- homographic dependence (not implemented yet with any force field)
+\item{2} -- hyperbolic tangent dependence \cite{liwo_2007}.
+\end{description}
+
+\item{DISTCHAINMAX} (50.0) -- for oligomeric proteins, distance between the chains
+ above which restraints will be switched on to keep the chains at a
+ reasonable distance.
+
+\item{PDBOUT} -- clusters will be printed in PDB format.
+
+\item{ECUT} -- energy cut-off criterion to print conformations (UNRES-CLUST runs).
+ Only those families will be output the energy of the lowest-energy
+ conformation of which is within ECUT kcal/mol above that of the
+ lowest-energy conformation and for a family only those members will be
+ output which have energy within ECUT kcal/mol above the energy of the
+ lowest-energy member of the family.
+
+\item{PRINT\_CART} -- output leading members of the families in UNRES x format.
+
+\item{PRINT\_INT} -- output leading members of the families in UNRES int format.
+
+\item{REF\_STR} -- if present, reference structure is input and rmsd will be computed
+ with respect to it (CLUST-UNRES only; rmsd is provided in the cx file
+ from WHAM for CLUST-WHAM runs).
+
+\item{PDBREF} -- if present, reference structure will be read in from a pdb file.
+
+\item{SIDE} -- side chains will be considered in superposition when calculating rmsd.
+
+\item{CA\_ONLY} -- only the Calpha atoms will be used in rmsd calculation.
+
+\item{NSTART} (0) -- first residue to superpose.
+
+\item{NEND} (0) -- last residue to superpose.
+
+\item{NTEMP} (1) -- number of temperatures at which probabilities will be calculated
+ and clustering performed (CLUST-WHAM).
+
+\item{TEMPER} (NTEMP tiles) -- temperatures at which clustering will be performed
+ (CLUST-WHAM).
+
+\item{EFREE} -- if present, conformation entropy factor is read if the conformation
+ is input from an x or pdb file.
+
+\item{PROB} (0.99) -- cut-off on the summary probability of the conformations that
+ are clustered at a given temperature (CLUST-WHAM).
+
+\item{IOPT} (2) - clustering algorithm:
+
+\begin{description}
+\item{1} -- Ward's minimum variance method.
+\item{2} -- single link method.
+\item{3} -- complete link method.
+\item{4} -- average link (or group average) method.
+\item{5} -- McQuitty's method.
+\item{6} -- Median (Gower's) method.
+\item{7} -- centroid method.
+\end{description}
+
+Instead of IOPT=1, MINTREE and instead of IOPT=2 MINVAR can be specified
+
+\item{NCUT} (1) -- number of cut-offs in clustering.
+
+\item{CUTOFF} (-1.0; NCUT values) cut-offs at which clustering will be performed;
+ at the cut-off flagged by a ``-'' sign clustering will be performed with
+ cutoff value=abs(cutoff(i)) and conformations corresponding to clusters
+ will be output in the desired format.
+
+\item{MAKE\_TREE} -- if present, produce a clustering-tree graph.
+
+\item{PLOT\_TREE} -- if present, the tree is written in PicTeX format to a file.
+
+\item{PRINT\_DIST} -- if present, distance (rmsd) matrix is printed to main output
+ file.
+
+\item{PUNCH\_DIST} -- if present, the upper-triangle of the distance matrix will be
+ printed to a file.
+\end{description}
+
+\subsubsection{Energy-term weights and parameter files}
+\label{sect:inoutfiles:main:weights}
+
+\begin{description}
+\item{WSC (1.0)} -- side-chain-side-chain interaction energy.
+
+\item{WSCP} (1.0) -- side chain-peptide group interaction energya.
+
+\item{WELEC} (1.0) -- peptide-group-peptide group interaction energy.
+
+\item{WEL\_LOC} (1.0) -- third-order backbone-local correlation energy.
+
+\item{WCORR} (1.0) -- fourth-order backbone-local correlation energy.
+
+\item{WCORR5} (1.0) -- fifth-order backbone-local correlation energy.
+
+\item{WCORR6} (1.0) -- sixth-order backbone-local correlation energy.
+
+\item{WTURN3} (1.0) -- third-order backbone-local correlation energy of pairs of
+ peptide groups separated by a single peptide group.
+
+\item{WTURN4} (1.0) -- fourth-order backbone-local correlation energy of pairs of
+ peptide groups separated by two peptide groups.
+
+\item{WTURN6} (1.0) -- sixth-order backbone-local correlation energy for pairs of
+ peptide groups separated by four peptide groups.
+
+\item{WBOND} (1.0) -- virtual-bond-stretching energy.
+
+\item{WANG} (1.0) -- virtual-bond-angle-bending energy.
+
+\item{WTOR} (1.0) -- virtual-bond-torsional energy.
+
+\item{WTORD} (1.0) -- virtual-bond-double-torsional energy.
+
+\item{WSCCOR} (1.0) -- sequence-specific virtual-bond-torsional energy.
+
+\item{WDIHC} (0.0) -- dihedral-angle-restraint energy.
+
+\item{WHPB} (1.0) -- distance-restraint energy.
+
+\item{SCAL14} (0.4) -- scaling factor of 1,4-interactions
+
+\end{description}
+
+\subsubsection{Molecule information}
+\label{sect:inoutfiles:main:molinfo}
+
+\paragraph{Sequence information\\ \\}
+\label{sect:inoutfiles:main:molinfo:sequence}
+
+Amino-acid sequence
+
+3-letter code: Sequence is input in format 20(1X,A3)
+
+1-letter code: Sequence is input in format 80A1
+
+\paragraph{Dihedral angle restraint information\\ \\}
+\label{sect:inoutfiles:molinfo:dihrestr}
+
+This is the information about dihedral-angle restraints, if any are present.
+It is specified only when WITH\_DIHED\_CONSTR is present in the first record.
+
+1st line: ndih\_constr -- number of restraints (free format)
+
+2nd line: ftors -- force constant (free format)
+
+Each of the following ndih\_constr lines:
+
+idih\_constr(i),phi0(i),drange(i) (free format)
+
+\begin{description}
+\item{idih\_constr(i)} -- the number of the dihedral angle gamma corresponding to the
+ith restraint
+
+\item{phi0(i)} -- center of dihedral-angle restraint
+
+\item{drange(i)} -- range of flat well (no restraints for phi0(i) +/- drange(i))
+
+\end{description}
+
+\paragraph{Disulfide-bridge data \\ \\}
+\label{sect:inoutfiles:molinfo:disulfide}
+
+1st line: NS, (ISS(I),I=1,NS) (free format)
+
+\begin{description}
+
+\item{NS} -- number of cystine residues forming disulfide bridges.
+
+\item{ISS(I)} -- the number of the Ith disulfide-bonding cystine in the sequence.
+
+\end{description}
+
+2nd line: NSS, (IHPB(I),JHPB(I),I=1,NSS) (free format)
+
+\begin{description}
+
+\item{NSS} -- number of disulfide bridges
+
+\item{IHPB(I),JHPB(I)} -- the first and the second residue of ith disulfide link.
+
+Because the input is in free format, each line can be split
+\end{description}
+
+\subsubsection{Reference structure}
+\label{sect:inoutfiles:molinfo:refstr}
+
+If PDBREF is specified, filename with reference (experimental) structure,
+otherwise UNRES internal coordinates as the theta, gamma, alpha, and beta
+angles.
+
+\subsection{Main output file}
+\label{sect:inoutfiles:mainoutput}
+
+The main (with name INPUT\_clust.out or INPUT\_clust.out\_000 for parallel runs)
+output file contains the results of clustering (numbers of families
+at different cut-off values, probabilities of clusters, composition of
+families, and rmsd values corresponding to families (0 if rmsd was not
+computed or read from WHAM-generated cx file).
+
+The output files corresponding to non-master processors
+(INPUT\_clust.out\_xxx where xxx$>$0 contain only the information up to the
+clustering protocol. These files can be deleted right after the run.
+
+Excerpts from the a sample output file are given below:
+
+CLUST-UNRES:
+
+\begin{verbatim}
+
+THERE ARE 20 FAMILIES OF CONFORMATIONS
+
+FAMILY 1 CONTAINS 2 CONFORMATION(S):
+ 42 -2.9384E+03 50 -2.9134E+03
+
+
+Max. distance in the family: 14.0; average distance in the family: 14.0
+
+FAMILY 2 CONTAINS 3 CONFORMATION(S):
+ 13 -2.9342E+03 7 -2.8827E+03 10 -2.8682E+03
+\end{verbatim}
+
+CLUST-WHAM:
+
+\begin{verbatim}
+AT CUTOFF: 200.00000
+Maximum distance found: 137.82
+Free energies and probabilities of clusters at 325.0 K
+clust efree prob sumprob
+ 1 -76.5 0.25035 0.25035
+ 2 -76.5 0.24449 0.49484
+ 3 -76.4 0.21645 0.71129
+ 4 -76.4 0.20045 0.91174
+ 5 -75.8 0.08826 1.00000
+
+
+THERE ARE 5 FAMILIES OF CONFORMATIONS
+
+FAMILY 1 WITH TOTAL FREE ENERGY -7.65228E+01 CONTAINS 548 CONFORMATION(S):
+8363 -7.332E+013939 -7.332E+012583 -7.332E+017395 -7.332E+019932 -7.332E+01
+5816 -7.332E+013096 -7.332E+012663 -7.332E+014099 -7.332E+016822 -7.332E+01
+3176 -7.332E+017542 -7.332E+018933 -7.332E+017315 -7.332E+01 200 -7.332E+01.
+.
+5637 -7.062E+018060 -7.061E+013797 -7.060E+018800 -7.057E+016295 -7.057E+01
+6298 -7.057E+012332 -7.057E+012709 -7.057E+01
+
+Max. distance in the family: 16.5; average distance in the family: 8.8
+Average RMSD 8.22 A
+\end{verbatim}
+
+\subsection{Output coordinate files}
+\label{sect:inoutfiles:outcoord}
+
+\subsubsection{The internal coordinate (int) files}
+\label{sect:inoutfiles:int}
+
+The file with name COORD\_clust.int contains the angles theta, gamma, alpha,
+and beta of all residues of the leaders (lowest UNRES energy conformations
+from consecutive families for CLUST-UNRES runs and lowest free energy
+conformations for CLUST-WHAM runs). The format is the same as that of the
+file output by UNRES; see section 9.1.1 of UNRES description.
+
+For CLUST-WHAM runs, the first line contains more items:
+
+\begin{tabular}{ll}
+number of family &(format i5)\\
+UNRES free energy of the conformation &(format f12.3)\\
+Free energy of the entire family &(format f12.3)\\
+number of disulfide bonds &(format i2)\\
+list disulfide-bonded pairs &(format 2i3)\\
+conformation class number (0 if not provided)&(format i10)\\
+\end{tabular}
+
+\subsubsection{The Cartesian coordinate (x) files}
+\label{sect:inoutfiles:card}
+
+The file with name COORD\_clust.x contains the Cartesian coordinates of the
+alpha-carbon and side-chain-center coordinates. The coordinate format is
+as in section 9.1.2 of UNRES description and the first line contains the
+following items:
+
+\begin{tabular}{ll}
+Number of the family &(format I5)\\
+UNRES free energy of the conformation &(format f12.3)\\
+Free energy of the entire family &(format f12.3)\\
+number of disulfide bonds &(format i2)\\
+list disulfide-bonded pairs &(format 2i3)\\
+conformation class number (0 if not provided)&(format i10)\\
+\end{tabular}
+
+\subsubsection{The PDB files}
+\label{sect:inoutfiles:PDB}
+
+The PDB files are in standard format (see
+\href{ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf}{ftp://ftp.wwpdb.org/pub/pdb/doc/format\_descriptions}).
+The ATOM records contain Calpha coordinates (CA) or UNRES side-chain-center
+coordinates (CB). For oligomeric proteins chain identifiers are present
+(A, B, ..., etc.) and each chain ends with a TER record. Coordinates of a
+single conformation or multiple conformations The header (REMARK) records
+and the contents depends on cluster run type. The next subsections are devoted
+to different run types.
+
+\paragraph{CLUST-UNRES runs \\ \\}
+\label{sect:inoutfiles:PDB:clust-unres}
+
+The files contain the members of the families obtained from clustering such
+that the lowest-energy conformation of a family is within ECUT kcal/mol higher
+in energy than the lowest-energy conformation. Again, within a family, only
+those conformations are output whose energy is within ECUT kcal/mol above
+that of the lowest-energy member of the family. Families and the members
+of a family within a family are ranked by increasing energy. The file names are:
+
+COORD\_xxxx.pdb where xxxx is the number of the family, if the family contains
+ only one member of if only one member is output.
+
+COORD\_xxxx\_yyy.pdb where xxxx is the number of the family and yyy is the number
+ of the member of this family.
+
+An example is the following:
+
+\begin{verbatim}
+REMARK R0001 ENERGY -2.93843E+03
+ATOM 1 CA GLY 1 0.000 0.000 0.000
+ATOM 2 CA HIS 2 3.800 0.000 0.000
+ATOM 3 CB HIS 2 5.113 1.656 0.015
+ATOM 4 CA VAL 3 5.927 -3.149 0.000
+.
+.
+.
+ATOM 346 CB GLU 183 -43.669 -32.853 -7.320
+TER
+CONECT 1 2
+CONECT 2 4 3
+.
+.
+.
+CONECT 341 343 342
+CONECT 343 344
+CONECT 345 346
+\end{verbatim}
+
+where ENERGY is the UNRES energy. The CONECT records defined the Calpha-Calpha
+and Calpha-SC connection.
+
+\paragraph{CLUST-WHAM runs\\ \\}
+\label{sect:inoutfiles:PDB:clust-wham}
+
+The program generates a file for each family with its members and a summary
+file with ensemble-averaged conformations for all families. These are described
+in the two next sections.
+
+\subparagraph{Conformation family files\\ \\}
+\label{sect:inoutfiles:PDB:clust-unres:family}
+
+For each family, the file name is COORD\_TxxxK\_yyyy.pdb, where yyyy is the
+number of the family and xxx is the integer part of the temperature (K).
+The first REMARK line in the file contains the information about the free
+energy and average rmsd of the entire cluster and, for each conformation,
+the initial REMARK line contains these quantities for this conformation.
+Same applies to oligomeric proteins, for which the TER records separate the
+chains and the ENDMDL record separates conformations.
+An example is given below.
+
+\begin{verbatim}
+REMARK CLUSTER 1 FREE ENERGY -7.65228E+01 AVE RMSD 8.22
+REMARK 1BDD L18G full clust ENERGY -7.33241E+01 RMS 10.40
+ATOM 1 CA VAL 1 18.059 -33.585 4.616 1.00 5.00
+ATOM 2 CB VAL 1 18.720 -32.797 3.592 1.00 5.00
+.
+.
+.
+ATOM 115 CA LYS 58 29.641 -44.596 -8.159 1.00 5.00
+ATOM 116 CB LYS 58 27.593 -45.927 -8.930 1.00 5.00
+TER
+CONECT 1 3 2
+CONECT 3 5 4
+.
+.
+CONECT 113 114
+CONECT 115 116
+TER
+REMARK 1BDD L18G full clust ENERGY -7.33240E+01 RMS 10.04
+ATOM 1 CA VAL 1 3.174 2.833 -34.386 1.00 5.00
+ATOM 2 CB VAL 1 3.887 2.811 -33.168 1.00 5.00
+.
+.
+ATOM 115 CA LYS 58 16.682 6.695 -20.438 1.00 5.00
+ATOM 116 CB LYS 58 18.925 5.540 -20.776 1.00 5.00
+TER
+CONECT 1 3 2
+CONECT 3 5 4
+CONECT 113 114
+CONECT 115 116
+TER
+\end{verbatim}
+
+\subparagraph{Average-structure file\\ \\}
+\label{sect:inoutfiles:PDB:clust-unres:average}
+
+The file name is COORD\_T\_xxxK\_ave.pdb. The entries are in pairs; the first
+one is cluster-averaged conformation and the second is a family member which
+has the lowest rmsd from this average conformation. Computing average
+conformations is explained in section 2.5 of ref 3. Example excerpts from
+an entry corresponding to a given family are shown below.
+
+\begin{verbatim}
+REMAR AVERAGE CONFORMATIONS AT TEMPERATURE 300.00
+REMARK CLUSTER 1
+REMARK 2HEP clustering 300K ENERGY -8.22572E+01 RMS 3.29
+ATOM 1 CA MET 1 -17.748 48.148 -19.284 1.00 5.96
+ATOM 2 CB MET 1 -17.373 47.911 -19.294 1.00 6.34
+ATOM 3 CA ILE 2 -18.770 49.138 -18.133 1.00 3.98
+.
+.
+.
+ATOM 80 CB PHE 41 -14.353 44.680 -15.642 1.00 2.62
+ATOM 81 CA ARG 42 -11.619 41.645 -13.117 1.00 4.06
+ATOM 82 CB ARG 42 -11.330 40.378 -13.313 1.00 5.19
+TER
+CONECT 1 3 2
+CONECT 3 5 4
+.
+.
+.
+CONECT 76 78 77
+CONECT 78 79
+CONECT 79 80
+CONECT 81 82
+TER
+REMARK 2HEP clustering 300K ENERGY -8.22572E+01 RMS 3.29
+ATOM 1 CA MET 1 -37.698 40.489 -32.408 1.00 5.96
+ATOM 2 CB MET 1 -38.477 39.426 -34.159 1.00 6.34
+.
+.
+.
+ATOM 80 CB PHE 41 -35.345 50.342 -31.371 1.00 2.62
+ATOM 81 CA ARG 42 -33.603 54.332 -27.130 1.00 4.06
+ATOM 82 CB ARG 42 -33.832 53.074 -24.415 1.00 5.19
+TER
+CONECT 1 3 2
+CONECT 3 5 4
+.
+.
+.
+CONECT 76 78 77
+CONECT 78 79
+CONECT 79 80
+CONECT 81 82
+TER
+\end{verbatim}
+
+\subsection{The conformation-distance file}
+\label{sect:inoutfiles:confdist}
+
+The file name is INPUT\_clust.rms. It contains the upper-diagonal part of
+the matrix of rmsds between conformations and differences between their
+energies:
+
+i,j,rmsd,energy(j)-energy(i) (format 2i5,2f10.5)
+
+where i and j, j$>$i are the numbers of the conformations, rmsd is the rmsd
+between conformation i and conformation j and energy(i) and energy(j) are
+the UNRES energies of conformations i and j, respectively.
+
+\subsection{The clustering-tree PicTeX file}
+\label{sect:inoutfiles:tree}
+
+This file contains the PicTeX code of the clustering tree. The file name is
+INPUT\_clust.tex. It should be supplemented with LaTeX preamble and final
+commands or incorporated into a LaTeX source and compiled with LaTeX. The
+picture is produced by running LaTeX followed by dvips, dvipdf or other command
+to convert LaTeX-generated dvi files into a human-readable files.
+
+\newpage
+
+\section{SUPPORT}
+\label{sect:support}
+
+ Dr. Adam Liwo\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ phone: +48 58 523 5124\\
+ fax: +48 58 523 5012\\
+ e-mail: \href{mailto:adam@sun1.chem.univ.gda.pl}{\textcolor{blue}{adam@sun1.chem.univ.gda.pl}}\\
+
+ Dr. Cezary Czaplewski\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ phone: +48 58 523 5126\\
+ fax: +48 58 523 5012\\
+ e-mail: \href{mailto:cezary.czaplewski@ug.edu.pl}{cezary.czaplewski@ug.edu.pl}
+
+
+Prepared by Adam Liwo, 02/19/12
+
+\LaTeX versioin, 09/28/12
+
+Revised by Adam Liwo, 12/04/14
+
+\end{document}
--- /dev/null
+\documentclass[12pt]{article}
+%\usepackage{latex2html}
+\usepackage{enumerate}
+\usepackage{longtable}
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{color}
+\parindent=0pt
+\parskip=12pt
+\textheight=24cm
+\textwidth=18cm
+\topmargin=-2.5cm
+\oddsidemargin=-0.5cm
+\setcounter{secnumdepth}{5}
+\setcounter{tocdepth}{5}
+\begin{document}
+\sloppy
+
+\title{XDRF2PDB, XDRF2PDB-M, XDRF2X\\
+Programs to convert compressed Cartesian coordinate files from UNRES into ASCII formats}
+
+\author{Laboratory of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Sobieskiego 18\\ 80-952 Gdansk, Poland\\
+\\
+\\
+Scheraga Group\\ Baker Laboratory of Chemistry \\
+and Chemical Biology\\ Cornell University\\ Ithaca, NY 14853-1301, USA}
+
+\maketitle
+
+%
+%TABLE OF CONTENTS
+%
+%1. License terms
+%2. Programs and their functions
+%3. Installation
+%4. Command lines and files
+% 4.1 xdrf2pdb
+% 4.2 xdrf2pdb-m
+% 4.3 xdrf2x
+% 4.4 xdrf2ang
+%5. Support
+%
+\newpage
+
+\section{LICENSE TERMS}
+\label{sect:license}
+
+\begin{itemize}
+
+\item
+ This software is provided free of charge to academic users, subject to the condition that no part of it be sold or used otherwise for commercial purposes, including, but not limited to its incorporation into commercial software packages, without written consent from the authors. For permission contact Prof. H. A. Scheraga, Cornell University.
+
+\item
+ This software package is provided on an ``as is'' basis. We in no way warrant either this software or results it may produce.
+
+\item
+ Reports or publications using this software package must contain an acknowledgment to the authors and the NIH Resource in the form commonly used in academic research.
+
+\end{itemize}
+
+\newpage
+
+\section{PROGRAMS AND THEIR FUNCTONS}
+\label{sect:programs}
+
+The following three programs can be used to extract conformations from compressed Cartesian (cx) files from UNRES:
+
+\begin{description}
+
+\item{xdrf2pdb} --- takes a single trajectory file and converts it into PDB format.
+
+\item{xdrf2pdb-m} -- takes a multiple-trajectory file from UNRES/MREMD simulations and enables the user to extract conformation of a particular trajectory and save them to a PDB file.
+
+\item{xdrf2x} -- takes a single trajectory file and converts it into UNRES Cartesian coordinate (x) format.
+
+\item{xdrf2ang} -- takes a single trajectory file and calculates UNRES backbone angles (theta and gamma).
+
+\end{description}
+
+\section{INSTALLATION}
+\label{sect:install}
+
+Run make all on your system to install all programs or make {\it program} to install a particular program. You might need to run make in the xdrf subdirectory beforehand or point to the xdrf library that is on another directory in the Makefile.
+
+The programs compile on all known Fortran compilers, including gfortran. It is recommeded to use Cmake
+to install whole package; please see Installation Guide.
+
+\section{COMMAND LINE AND FILES}
+\label{sect:command}
+
+For xdrf2pdb and xdrf2pdb-m, you'll need to prepare the UNRES sequence file in either one- or three-letter code.
+
+\subsection{XDRF2PDB}
+\label{sect:command:xdrf2pdb}
+
+Command line syntax:
+
+xdrf2pdb one/three seqfile cxfile [freq] [start] [end] [pdbfile]
+
+\begin{description}
+
+\item{one or three} indicates in what format the sequence will be read
+\item{seqfile} -- the file with the sequence:
+\begin{itemize}
+\item one-letter format: 80A1
+\item three-letter format: 20(A3,1X)
+\end{itemize}
+Note that the sequence must match exactly the UNRES sequence.
+\item{cxfile} -- full name of the trajectory file with compressed Cartesian coordinates.
+\item{freq} (1) -- conformation sampling frequency (each freq-th conformation will be saved to PBD file.
+\item{start} (1) -- the first conformation to be saved to PDB file.
+\item{end} (1000000000) -- the last conformation to be saved to PDB file.
+\item{pdbfile} (cxfile with extension changed from cx to pdb) -- the output PDB file.
+
+\end{description}
+
+\subsection{XDRF2PDB-M}
+\label{sect:command:xdrf2pdb-m}
+
+Command line syntax:
+
+xdrf2pdb-m one/three seqfile cxfile [ntraj] [itraj] [pdbfile] [ifreq]
+
+\begin{description}
+
+\item{cxfile} - the name of the compressed trajectory file from an UNRES/MREMD run carried out with TRAJ1FILE (conformations from all trajectories output to a single file).
+\item{ntraj} (1) -- number of trajectories in the multi-trajectory run.
+\item{itraj} (1) -- the number of trajectory to be extracted.
+
+\end{description}
+
+\subsection{XDRF2X}
+\label{sect:command:xdrf2x}
+
+Command line syntax:
+
+xdrf2x cxfile [is] [ie] [freq] $>$ x\_file
+
+The meaning of the the arguments is as in section
+\ref{sect:command:xdrf2pdb}; the conformations are output in UNRES Cartesian coordinate format to stdout.
+
+\subsection{XDRF2ANG}
+\label{sect:command:xdrf2ang}
+
+Command line syntax:
+
+xdrf2ang one/three seqfile cxfile [freq] [start] [end] [angfile]
+
+The meaning of the first six parameters is as in section \ref{sect:command:xdrf2pdb} angfile is
+ the name of the output angle file; is assigned cx file name with the cx
+ extension changed to ang, if not present.
+
+\section{SUPPORT}
+\label{sect:support}
+
+ Dr. Adam Liwo\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ phone: +48 58 523 5124\\
+ fax: +48 58 523 5012\\
+ e-mail: \href{mailto:adam@sun1.chem.univ.gda.pl}{\textcolor{blue}{adam@sun1.chem.univ.gda.pl}}\\
+
+
+
+ Dr. Cezary Czaplewski\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ phone: +48 58 523 5126\\
+ fax: +48 58 523 5012\\
+ e-mail: \href{mailto:cezary.czaplewski@ug.edu.pl}{cezary.czaplewski@ug.edu.pl}
+
+Prepared by Adam Liwo, 11/26/11
+
+\LaTeX version, 09/28/12
+
+Revised by Adam Liwo, 12/04/14
+
+\end{document}
--- /dev/null
+\documentclass[12pt]{article}
+%\usepackage{latex2html}
+\usepackage{enumerate}
+\usepackage{longtable}
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{color}
+\parindent=0pt
+\parskip=12pt
+\textheight=24cm
+\textwidth=18cm
+\topmargin=-2.5cm
+\oddsidemargin=-0.5cm
+\setcounter{secnumdepth}{5}
+\setcounter{tocdepth}{5}
+\begin{document}
+\sloppy
+
+\title{UNRES.3.2.1 -- INSTALLATION GUIDE}
+
+\author{Dawid Jagie{\l}a, Adam Liwo\\ Laboratory of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Wita Stwosza 63\\ 80-308 Gdansk, Poland}
+
+\maketitle
+
+\newpage
+
+\tableofcontents
+
+\newpage
+
+\section{Putting the package on your system}
+\label{section:put}
+
+The distribution is contained in the unrespack-v.3.2.1.tar.gz file. To put the package
+on your system, copy the archive to your UNRES directory (you might want to create
+an environmental variable, \$UNRESROOT or so, to define the location of UNRES on
+your system) and say:
+
+\begin{verbatim}
+gzip -cd unrespack-v.3.2.1.tar.gz | tar xf -
+\end{verbatim}
+
+This will produce the directory structure shown in Figure \ref{fig:distr}.
+
+\begin{figure}
+{\small
+\begin{verbatim}
+$UNRESROOT
+ |
+ |---------doc (documentation)
+ |
+ |---------PARAM (force field parameters)
+ |
+ |---------source
+ | |
+ | |-----unres (UNRES source codes; various versions)
+ | | |
+ | | |---src_MIN (only energy evaluation and minimization)
+ | | |---src_CSA (all functions except MD, includes CSA)
+ | | |---src_MD (all functions except CSA, includes MD, single chains)
+ | | |---src_MD-M (all functions except CSA, includes MD, oligomeric proteins)
+ | |-----wham (weighted analysis method source codes)
+ | | |
+ | | |---src (single chains)
+ | | |---src-M (oligomeric proteins)
+ | |
+ | |-----cluster (cluster analysis source coded)
+ | | |
+ | | |---clust-unres
+ | | | |
+ | | | |----src (input data from UNRES)
+ | | |
+ | | |---clust-wham (input data from WHAM)
+ | | |
+ | | |----src (for single-chain proteins)
+ | | |----src-M (for oligomeric proteins)
+ | |
+ | |-----xdrfpdb (file format conversion source codes)
+ | |
+ | |---src (single chains)
+ | |---src-M (oligomers)
+ |
+ |----------bin (C-shell script, batch scripts, and pre-compiled binaries)
+ | |
+ | |-----unres
+ | | |
+ | | |---CSA
+ | | |---MD
+ | |
+ | |-----wham
+ | |-----cluster
+ | |-----xdrfpdb
+ |
+ |--------examples
+ |
+ |-----unres
+ |-----wham
+ |-----cluster
+\end{verbatim}
+}
+\caption{Directory structure of the unres-3.2.1 package}
+\label{fig:distr}
+\end{figure}
+
+\section{Installation options}
+\label{sect:general}
+
+The most convenient way to install the package is using Cmake, as described
+in section 2. If your system does not run the required version of Cmake or
+installation does not work, do step-by-step compilation of the components
+of the package, as described in section 3.
+
+\subsection{Requirements}
+
+\begin{description}
+\item{--} C compiler
+\item{--} Fortran compiler (must understant the Fortran 77 instructions)
+\item{--} MPI (for CSA and MREMD)
+\end{description}
+
+\section{Installation using Cmake}
+\label{section:Cmake}
+
+\subsection{Requirements}
+
+\begin{description}
+\item{--} CMake 2.8.0 or later
+\item{--} C compiler
+\item{--} Fortran compiler
+\item{--} MPI (for CSA and MREMD)
+\end{description}
+
+\subsection{Basic installation}
+
+These instructions give a very basic overview of how to configure, compile and
+install UNRESPACK on most systems. If you are using unique install locations
+and/or libraries that are not automatically detected please consult the 'Advanced'
+section.
+
+\begin{enumerate}
+
+\item
+Create a 'build' directory in the package source directory.
+
+\begin{verbatim}
+ mkdir build
+ cd build
+\end{verbatim}
+
+\item
+Configure the build system
+
+\begin{verbatim}
+ cmake ..
+\end{verbatim}
+
+\item
+Compile
+
+\begin{verbatim}
+ make
+\end{verbatim}
+
+\item
+Install
+
+\begin{verbatim}
+ sudo make install
+\end{verbatim}
+
+\noindent or
+
+\begin{verbatim}
+ make install
+\end{verbatim}
+
+\end{enumerate}
+
+\subsection{Advanced installation}
+
+The build system (CMake) provides mechanisms for specifying non-standard
+build parameters.
+
+\begin{enumerate}
+
+\item
+\underline{Compilers \& installation}
+
+\begin{verbatim}
+ -DCMAKE_Fortran_COMPILER=xxx equal to name of Fortran Compiler you wish to use
+ (ifort, gfortran)
+
+ -DCMAKE_INSTALL_PREFIX=xxx specify the binaries installation prefix
+ (default UNRESPACK_source_dir/bin)
+\end{verbatim}
+
+\item
+\underline{Force fields}
+
+\begin{verbatim}
+ -DUNRES_MD_FF=xxx compiles the MD versions with given force field.
+ Options are: GAB, E0LL2Y. Default: GAB
+
+ -DUNRES_CSA_FF=xxx compiles the CSA versions with given force field
+ Options are: CASP3, ALPHA, BETA, ALPHABETA, CASP5, 3P, 4P. Default: 4P.
+\end{verbatim}
+
+Please read the online documentation on force fields available at
+ http://unres.eu/unres\#SECTION00090000000000000000
+
+
+\item
+\underline{MPI}
+
+MPI implementation on your system should be automatically detected ("MPI Found"
+message after runing cmake). If not you have two options:
+
+\begin{enumerate}
+
+\item
+Try setting the path to you MPI wrapper implementation
+
+\begin{verbatim}
+ -DMPI_Fortran_COMPILER=xxx MPI wrapper
+\end{verbatim}
+
+\item
+If option 1 fails or your MPI implementation does not come with a compiler wrapper
+ try setting both the MPI include and library paths manually. This will circumvent
+ autodetection entirely.
+
+\begin{verbatim}
+ -DMPI_Fortran_INCLUDE_PATH=xxx
+ -DMPI_Fortran_LIBRARY="xxx"
+\end{verbatim}
+
+\end{enumerate}
+\end{enumerate}
+
+\section{Step-by-step installation}
+\label{sect:stepbystep}
+
+For this installation, you will need to visit each source directory (see doc/UNRESPACK.txt
+for directory structure). Specific installation instructions are in the documentation of
+of the particular components of the package (UNRES, WHAM, CLUSTER, XDRFPDB). Only general
+instructions are given here.
+
+\begin{enumerate}
+
+\item
+Go to the respective source directory.
+
+\item
+Determine if any of the Makefiles present there matches your needs. The Makefiles for
+Intel Fortran and Gnu Fortran are present everywhere and are guaranteed to work (provided
+that your compiler/MPI installation is correct). Use this Makefile as the working Makefile
+
+If your system uses a different compiler, copy the most matching Makefile to your working
+Makefile (e.g., to Makefile\_CRAY if you'll be working with Cray Fortran).
+
+\item
+Make a symbolic link of the working Makefile to Makefile, e.g.,
+
+\begin{verbatim}
+ln -s Makefile_gfortran Makefile
+\end{verbatim}
+
+Before that, you'll need to remove the existing symbolic link (in the distribution, it
+points to Makefile\_ifort).
+
+\item
+Edit the Makefile to define MPI location, libraries, and the binaries directory
+and executalble names, if you want to use different location/names from those in the
+distribution Makefiles. The present locations are the subdirectories of the bin
+directory and executable names include package component, compiler, MPI information,
+and force field, e.g. unres\_csa\_gfort\_MPICH\_4P.exe stands for the CSA component,
+compiled with GNU Fortran in a parallel mode (using MPICH) to run calculations with
+the 4P force field.
+
+\item
+For the components of XDRFPDB and in the directory cluster/unres/src, say
+
+\begin{verbatim}
+make
+\end{verbatim}
+
+In other directories say
+
+\begin{verbatim}
+make <force_field>
+\end{verbatim}
+
+to create the respective executable.
+
+The compiler flags are specified for the 4P (also covers the 3P, and CASP5 ff),
+GAB (also covers E0G), and E0LL2Y force fields for all components; the CASP3 force field
+is also specified for the CSA and MINIM component.
+\end{enumerate}
+
+\section{TECHNICAL SUPPORT CONTACT INFORMATION}
+\label{sect:support}
+
+ Dawid Jagie{\l}a\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ fax: +48 58 523 5012\\
+ e-mail: \href{mailto:lightnir@gmail.com}{lightnir@gmail.com}\\
+
+\small{
+ Prepared by Dawid Jagie{\l}a and Adam Liwo, 4/12/2014\\
+}
+
+\end{document}
--- /dev/null
+\documentclass[12pt]{article}
+%\usepackage{latex2html}
+\usepackage{enumerate}
+\usepackage{longtable}
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{color}
+\parindent=0pt
+\parskip=12pt
+\textheight=24cm
+\textwidth=18cm
+\topmargin=-2.5cm
+\oddsidemargin=-0.5cm
+\setcounter{secnumdepth}{5}
+\setcounter{tocdepth}{5}
+\begin{document}
+\sloppy
+
+\title{UNRES - A PROGRAM FOR COARSE-GRAINED SIMULATIONS OF PROTEINS}
+
+\author{Laboratory of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Sobieskiego 18\\ 80-952 Gdansk, Poland\\
+\\
+\\
+Scheraga Group\\ Baker Laboratory of Chemistry \\
+and Chemical Biology\\ Cornell University\\ Ithaca, NY 14853-1301, USA}
+
+\maketitle
+
+\newpage
+
+\tableofcontents
+
+%TABLE OF CONTENTS
+%
+%1. License terms
+%2. Credits
+%3. General information
+% 3.1. Purpose
+% 3.2. Functions of the program
+% 3.3. Companion programs
+% 3.4. Programming language
+% 3.5. References
+%4. Installation
+%5. Customizing your batch and C-shell script
+%6. Command line and files
+%7. Force fields
+%8. Input files
+% 8.1. Main input data file
+% 8.1.1 Title
+% 8.1.2. Control data (data list format; READ_CONTROL subroutine)
+% 8.1.2.1 Keywords to chose calculation type
+% 8.1.2.2 Specification of protein and structure output in non-MD applications
+% 8.1.2.3. Miscellaneous
+% 8.1.3. Minimizer options (data list, subroutine READ_MINIM)
+% 8.1.4. CSA control parameters
+% 8.1.5. MCM data (data list, subroutine MCMREAD)
+% 8.1.6. MD data (subroutine READ_MDPAR)
+% 8.1.7. REMD/MREMD data (subroutine READ_REMDPAR)
+% 8.1.8. Energy-term weights (data list; subroutine MOLREAD)
+% 8.1.9. Input and/or reference PDB file name (text format; subroutine MOLREAD)
+% 8.1.10. Amino-acid sequence (free and text format)
+% 8.1.11. Disulfide-bridge information (free format; subroutine READ_BRIDGE)
+% 8.1.12. Dihedral-angle restraint data (free format; subroutine MOLREAD)
+% 8.1.13. Distance restraints (subroutine READ_DIST_CONSTR)
+% 8.1.14. Internal coordinates of the reference structure (free format; subroutine READ_ANGLES)
+% 8.1.15. Internal coordinates of the initial conformation (free format; subroutine READ_ANGLES)
+% 8.1.15.1. File name with internal coordinates of the conformations to be processed
+% 8.1.16 Control data for energy map construction (data lists; subroutine MAP_READ)
+% 8.2. Input coordinate files
+% 8.3. Other input files
+%9. Output files
+% 9.1. Coordinate files
+% 9.1.1. The internal coordinate (INT) files
+% 9.1.2. The plain Cartesian coordinate (X) files
+% 9.1.3. The compressed Cartesian coordinate (CX) files
+% 9.1.4. The Brookhaven Protein Data Bank format (PDB) files
+% 9.1.5. The SYBYLL (MOL2) files
+% 9.2. The summary (STAT) file
+% 9.2.1. Non-MD runs
+% 9.2.2. MD and MREMD runs
+% 9.3. CSA-specific output files
+%10. Technical support contact information
+%
+
+\newpage
+
+\section{LICENSE TERMS}
+\label{sect:license}
+
+\begin{itemize}
+
+\item
+ This software is provided free of charge to academic users, subject to the condition that no part of it be sold or used otherwise for commercial purposes, including, but not limited to its incorporation into commercial software packages, without written consent from the authors. For permission contact Prof. H. A. Scheraga, Cornell University.
+
+\item
+ This software package is provided on an ``as is'' basis. We in no way warrant either this software or results it may produce.
+
+\item
+ Reports or publications using this software package must contain an acknowledgment to the authors and the NIH Resource in the form commonly used in academic research.
+
+\end{itemize}
+
+\newpage
+
+\section{CREDITS}
+\label{sect:credits}
+
+The current and former developers of UNRES are listed in this section in alphabetic
+order together with their current or former affiliations.
+
+{\obeylines
+Maurizio Chinchio (formerly Cornell Univ., USA)
+Cezary Czaplewski (Univ. of Gdansk, Poland)
+Carlo Guardiani (Georgia State Univ., USA)
+Yi He (Cornell Univ., USA)
+Justyna Iwaszkiewicz (Swiss Institute of Bioinformatics, Switzerland)
+Dawid Jagiela (Univ. of Gdansk, Poland)
+Stanislaw Jaworski (deceased)
+Sebastian Kalinowski (Univ. of Gdansk, Poland)
+Urszula Kozlowska (deceased)
+Pawel Krupa (Univ. of Gdansk, Poland)
+Rajmund Kazmierkiewicz (Univ. of Gdansk, Poland)
+Jooyoung Lee (Korea Institute for Advanced Studies, Korea)
+Adam Liwo (Univ. of Gdansk, Poland)
+Mariusz Makowski (Univ. of Gdansk, Poland)
+Magdalena Mozolewska (Univ. of Gdansk, Poland)
+Marian Nanias (formerly Cornell Univ., USA)
+Stanislaw Oldziej (Univ. of Gdansk, Poland)
+Jaroslaw Pillardy (Cornell Univ., USA)
+Shelly Rackovsky (Mout Sinai School of Medicine, USA)
+Daniel Ripoll (formerly Cornell Univ., USA)
+Jeff Saunders (Schrodinger Inc., USA)
+Harold A. Scheraga (Cornell Univ., USA)
+Hujun Shen (Dalian Institute of Chemical Physics, P.R. China)
+Adam Sieradzan (Univ. of Gdansk, Poland)
+Ryszard Wawak (formerly Cornell Univ., USA)
+Tomasz Wirecki (Univ. of Gdansk, Poland)
+Marta Wisniewska (Univ. of Gdansk, Poland)
+Yanping Yin (Cornell Univ., USA)
+Bartlomiej Zaborowski (Univ. of Gdansk, Poland)
+}
+
+\newpage
+
+\section{GENERAL INFORMATION}
+\label{sect:geninfo}
+
+\subsection{Purpose}
+\label{sect:geninfo:purpose}
+
+Run coarse-grained calculations of polypeptide chains with the UNRES force field.
+There are two versions of the package which should be kept separate because of
+non-overlapping functions: version which runs global optimization (Conformational
+Space Annealing, CSA) and version that runs coarse-grained molecular dynamics and
+its extension. Because the installation, input file preparation and running CSA
+and MD versions are similar, a common manual is provided. Items specific
+for the CSA and MD version are marked ``CSA'' and ``MD'', respectively.
+
+MD version can be used to run multiple-chain proteins (however, that version of
+the code is a new release and might fail if yet un-checked functions are used).
+The multi-chain CSA version for this purpose is another package (written largely in
+C++).
+
+\subsection{Functions of the program}
+\label{sect:geninfo:functions}
+
+\begin{enumerate}
+
+\item
+ Perform energy evaluation of a single or multiple conformations (serial and parallel) (CSA and MD).
+
+\item
+ Run canonical mesoscopic molecular dynamics (serial and parallel) (MD).
+
+\item
+ Run replica exchange (REMD) and multiplexing replica exchange (MREMD) dynamics (parallel only) (MD).
+
+\item
+ Run multicanonical molecular dynamics (parallel only) (MD).
+
+\item
+ Run energy minimization (serial and parallel) (CSA and MD).
+
+\item
+ Run conformational space annealing (CSA search) (parallel only) (CSA).
+
+\item
+ Run Monte Carlo plus Minimization (MCM) (parallel only) (CSA).
+
+\item
+ Run conformational family Monte Carlo (CFMC) calculations (CSA).
+
+\item
+ Thread the sequence against a database from the PDB and minimize energy of each structure (CSA).
+
+\end{enumerate}
+
+Energy and force evaluation is parallelized in MD version.
+
+
+\subsection{Companion programs}
+\label{sect:geninfo:companion}
+
+The structures produced by UNRES can be used as inputs to the following programs provided
+with this package or separately:
+
+\begin{description}
+
+\item{xdrf2pdb} -- converts the compressed coordinate files from MD (but not MREMD)runs into
+ PDB format.
+
+\item{xdrf2pdb-m} -- same for MREMD runs (multiple trajectory capacity).
+
+\item{xdrf2x} -- converts the plain Cartesian coordinate files into PDB format.
+
+\item{WHAM} -- processes the coordinate files from MREMD runs and computes temperature profiles
+ of ensemble averages and computes the probabilities of conformations at selected
+ temperatures; also prepares data for CLUSTER and ZSCORE.
+
+\item{CLUSTER} -- does the cluster analysis of the conformations; for MREMD runs takes the
+ coordinate files from WHAM which contain information to compute probabilities
+ of conformations at any temperature.
+
+\item{PHOENIX} -- conversion of UNRES conformations to all-atom conformations.
+
+\item{ZSCORE} -- force field optimization (for developers).
+
+\end{description}
+
+Please consult the manuals of the corresponding packages for details. Note that not
+all of these packages are released yet; they will be released depending on their
+readiness for distribution. Contact Adam Liwo, Cezary Czaplewski or Stanislaw Oldziej
+for developmental versions of these programs.
+
+\subsection{Programming language}
+\label{sect:geninfo:language}
+
+This version of UNRES is written almost exclusively in Fortran 77; some subroutines
+for data management are in ansi-C. The package was parallelized with MPI.
+
+\newpage
+
+\subsection{References}
+\label{sect:geninfo:references}
+
+Citing the following references in your work that makes use of UNRES is gratefully
+acknowledged:
+
+\begingroup
+\renewcommand{\section}[2]{}%
+\begin{thebibliography}{10}
+
+\bibitem{liwo_1997}
+ A. Liwo, S. Oldziej, M.R. Pincus, R.J. Wawak, S. Rackovsky, H.A. Scheraga.
+ A united-residue force field for off-lattice protein-structure simulations.
+ I: Functional forms and parameters of long-range side-chain interaction potentials
+ from protein crystal data. {\it J. Comput. Chem.}, {\bf 1997}, 18, 849-873.
+
+\bibitem{liwo_1997_02}
+ A. Liwo, M.R. Pincus, R.J. Wawak, S. Rackovsky, S. Oldziej, H.A. Scheraga.
+ A united-residue force field for off-lattice protein-structure simulations.
+ II: Parameterization of local interactions and determination
+ of the weights of energy terms by Z-score optimization.
+ {\it J. Comput. Chem.}, {\bf 1997}, 18, 874-887.
+
+\bibitem{liwo_1997_03}
+A. Liwo, S. O{\l}dziej, R. Ka\'zmierkiewicz, M. Groth, C. Czaplewski.
+Design of a knowledge-based force field for off-lattice simulations of protein
+structure.
+{\it Acta Biochim. Pol.}, {\bf 1997}, 44, 527-548.
+
+
+\bibitem{liwo_1998}
+ A. Liwo, R. Kazmierkiewicz, C. Czaplewski, M. Groth, S. Oldziej, R.J. Wawak,
+ S. Rackovsky, M.R. Pincus, H.A. Scheraga.
+ United-residue force field for off-lattice protein-structure simulations.
+ III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials.
+ {\it J. Comput. Chem.}, {\bf 1998}, 19, 259-276.
+
+\bibitem{liwo_2001}
+ A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Cumulant-based expressions for the multibody terms for the correlation between
+ local and electrostatic interactions in the united-residue force field.
+ {\it J. Chem. Phys.}, {\bf 2001}, 115, 2323-2347.
+
+\bibitem{lee_2001}
+ J. Lee, D.R. Ripoll, C. Czaplewski, J. Pillardy, W.J. Wedemeyer, H.A. Scheraga,
+ Optimization of parameters in macromolecular potential energy functions by
+ conformational space annealing. {\it J. Phys. Chem. B}, {\bf 2001}, 105, 7291-7298
+
+\bibitem{pillardy_2001}
+ J. Pillardy, C. Czaplewski, A. Liwo, W.J. Wedemeyer, J. Lee, D.R. Ripoll,
+ P. Arlukowicz, S. Oldziej, Y.A. Arnautova, H.A. Scheraga,
+ Development of physics-based energy functions that predict medium-resolution
+ structures for proteins of the $\alpha, \beta$, and $\alpha/\beta$ structural classes.
+ {\it J. Phys. Chem. B}, {\bf 2001}, 105, 7299-7311
+
+\bibitem{liwo_2002}
+ A. Liwo, P. Arlukowicz, C. Czaplewski, S. Oldziej, J. Pillardy, H.A. Scheraga.
+ A method for optimizing potential-energy functions by a hierarchical design
+ of the potential-energy landscape: Application to the UNRES force field.
+ {\it Proc. Natl. Acad. Sci. U.S.A.}, {\bf 2002}, 99, 1937-1942.
+
+\bibitem{saunders_2003}
+ J. A. Saunders and H.A. Scheraga.
+ Ab initio structure prediction of two $\alpha$-helical oligomers
+ with a multiple-chain united-residue force field and global search.
+ {\it Biopolymers}, {\bf 2003}, 68, 300-317.
+
+\bibitem{saunders_2003_02}
+ J.A. Saunders and H.A. Scheraga.
+ Challenges in structure prediction of oligomeric proteins at the united-residue
+ level: searching the multiple-chain energy landscape with CSA and CFMC procedures.
+ {\it Biopolymers}, {\bf 2003}, 68, 318-332.
+
+\bibitem{oldziej_2003}
+ S. Oldziej, U. Kozlowska, A. Liwo, H.A. Scheraga.
+ Determination of the potentials of mean force for rotation about C$^\alpha$-C$^\alpha$
+ virtual bonds in polypeptides from the ab initio energy surfaces of terminally
+ blocked glycine, alanine, and proline. {\it J. Phys. Chem. A}, {\bf 2003}, 107, 8035-8046.
+
+\bibitem{liwo_2004}
+ A. Liwo, S. Oldziej, C. Czaplewski, U. Kozlowska, H.A. Scheraga.
+ Parameterization of backbone-electrostatic and multibody contributions
+ to the UNRES force field for protein-structure prediction from ab initio
+ energy surfaces of model systems. {\it J. Phys. A}, {\bf 2004}, 108, 9421-9438.
+
+\bibitem{oldziej_2004}
+ S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 2. Off-lattice tests of the method with single
+ proteins. {\it J. Phys. Chem. B.}, {\bf 2004}, 108, 16934-16949.
+
+\bibitem{oldziej_2004_02}
+ S. Oldziej, J. Lagiewka, A. Liwo, C. Czaplewski, M. Chinchio,
+ M. Nanias, H.A. Scheraga.
+ Optimization of the UNRES force field by hierarchical design of the
+ potential-energy landscape. 3. Use of many proteins in optimization.
+ {\it J. Phys. Chem. B.}, {\bf 2004}, 108, 16950-16959.
+
+\bibitem{oldziej_2004_03}
+ M. Khalili, A. Liwo, F. Rakowski, P. Grochowski, H.A. Scheraga.
+ Molecular dynamics with the united-residue model of polypeptide chains.
+ I. Lagrange equations of motion and tests of numerical stability in the
+ microcanonical mode, {\it J. Phys. Chem. B}, {\bf 2005}, 109, 13785-13797.
+
+\bibitem{khalili_2005}
+ M. Khalili, A. Liwo, A. Jagielska, H.A. Scheraga.
+ Molecular dynamics with the united-residue model of polypeptide chains.
+ II. Langevin and Berendsen-bath dynamics and tests on model $\alpha$-helical
+ systems. {\it J. Phys. Chem. B}, {\bf 2005}, 109, 13798-13810.
+
+\bibitem{khalili_2005_02}
+ A. Liwo, M. Khalili, H.A. Scheraga.
+ Ab initio simulations of protein-folding pathways by molecular dynamics with
+ the united-residue model of polypeptide chains.
+ {\it Proc. Natl. Acad. Sci. U.S.A.}, {\bf 2005}, 102, 2362-2367.
+
+\bibitem{rakowski_2006}
+ F. Rakowski, P. Grochowski, B. Lesyng, A. Liwo, H. A. Scheraga.
+ Implementation of a symplectic multiple-time-step molecular dynamics algorithm,
+ based on the united-residue mesoscopic potential energy function.
+ {\it J. Chem. Phys.}, {\bf 2006}, 125, 204107.
+
+\bibitem{nanias_2006}
+ M. Nanias, C. Czaplewski, H.A. Scheraga.
+ Replica exchange and multicanonical algorithms with the coarse-grained
+ united-residue (UNRES) force field.
+ {\it J. Chem. Theory and Comput.}, {\bf 2006}, 2, 513-528.
+
+\bibitem{liwo_2007}
+ A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, K. Wachucik, H.A. Scheraga.
+ Modification and optimization of the united-residue (UNRES) potential energy
+ function for canonical simulations. I. Temperature dependence of the effective
+ energy function and tests of the optimization method with single training
+ proteins.
+ {\it J. Phys. Chem. B}, {\bf 2007}, 111, 260-285.
+
+\bibitem{kozlowska_2007}
+ U. Kozlowska, A. Liwo, H.A. Scheraga.
+ Determination of virtual-bond-angle potentials of mean force for coarse-grained
+ simulations of protein structure and folding from ab initio energy surfaces of
+ terminally-blocked glycine, alanine, and proline.
+ {\it J. Phys.: Condens. Matter}, {\bf 2007}, 19, 285203.
+
+\bibitem{chichio_2007}
+ M. Chinchio, C. Czaplewski, A. Liwo, S. Oldziej, H.A. Scheraga.
+ Dynamic formation and breaking of disulfide bonds in molecular dynamics
+ simulations with the UNRES force field.
+ {\it J. Chem. Theory Comput.}, {\bf 2007}, 3, 1236-1248.
+
+\bibitem{rojas_2007}
+ A.V. Rojas, A. Liwo, H.A. Scheraga.
+ Molecular dynamics with the united-residue force field: Ab Initio folding
+ simulations of multichain proteins.
+ {\it J. Phys. Chem. B}, {\bf 2007}, 111, 293-309.
+
+\bibitem{liwo_2008}
+ A. Liwo, C. Czaplewski, S. Oldziej, A.V. Rojas, R. Kazmierkiewicz,
+ M. Makowski, R.K. Murarka, H.A. Scheraga.
+ Simulation of protein structure and dynamics with the coarse-grained UNRES
+ force field. In: Coarse-Graining of Condensed Phase and Biomolecular
+ Systems., ed. G. Voth, Taylor \& Francis, 2008, Chapter 8, pp. 107-122.
+
+\bibitem{czaplewski_2009}
+ C. Czaplewski, S. Kalinowski, A. Liwo, H.A. Scheraga.
+ Application of multiplexed replica exchange molecular dynamics
+ to the UNRES force field: tests with $\alpha$ and $\alpha+\beta$ proteins.
+ {\it J. Chem. Theory Comput.}, {\bf 2009}, 5, 627-640.
+
+\bibitem{he_2009}
+ Y. He, Y. Xiao, A. Liwo, H.A. Scheraga.
+ Exploring the parameter space of the coarse-grained UNRES force field by random
+ search: selecting a transferable medium-resolution force field.
+ {\it J. Comput. Chem.}, {\bf 2009}, 30, 2127-2135.
+
+\bibitem{kozlowska_2010}
+ U. Kozlowska, A. Liwo. H.A. Scheraga.
+ Determination of side-chain-rotamer and side-chain and backbone
+ virtual-bond-stretching potentials of mean force from AM1 energy surfaces of
+ terminally-blocked amino-acid residues, for coarse-grained simulations of
+ protein structure and folding. 1. The Method.
+ {\it J. Comput. Chem.}, {\bf 2010}, 31, 1143-1153.
+
+\bibitem{kozlowska_2010_02}
+ U. Kozlowska, G.G. Maisuradze, A. Liwo, H.A. Scheraga.
+ Determination of side-chain-rotamer and side-chain and backbone
+ virtual-bond-stretching potentials of mean force from AM1 energy surfaces of
+ terminally-blocked amino-acid residues, for coarse-grained simulations of
+ protein structure and folding. 2. Results, comparison with statistical
+ potentials, and implementation in the UNRES force field.
+ {\it J. Comput. Chem.}, {\bf 2010}, 31, 1154-1167.
+
+\bibitem{liwo_2010}
+ A. Liwo, S. Oldziej, C. Czaplewski, D.S. Kleinerman, P. Blood, H.A. Scheraga.
+ Implementation of molecular dynamics and its extensions with the coarse-grained
+ UNRES force field on massively parallel systems; towards millisecond-scale
+ simulations of protein structure, dynamics, and thermodynamics.
+ {\it J. Chem. Theory Comput.}, {\bf 2010}, 6, 890-909.
+
+\bibitem{sieradzan_2012}
+A.K. Sieradzan, U.H.E. Hansmann, H.A. Scheraga, A. Liwo.
+Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.
+{\it J. Chem. Theory Comput.}, {\bf 2012}, 8, 4746-4757.
+
+\bibitem{krupa_2013}
+P. Krupa, A.K. Sieradzan, S. Rackovsky, M. Baranowski, S. O{\l}dziej,
+H.A. Scheraga, A. Liwo, C. Czaplewski.
+Improvement of the treatment of loop structures in the UNRES
+force field by inclusion of coupling between backbone- and
+side-chain-local conformational states
+{\it J. Chem. Theory Comput.}, {\bf 2013}, 4620-4632.
+
+\bibitem{sieradzan_2014}
+A.K. Sieradzan, A. Niadzvedtski, H.A. Scheraga, A. Liwo.
+Revised backbone-virtual-bond-angle potentials to treat the L- and D-amino
+acid residues in the coarse-grained united residue (UNRES) force field.
+{\it J. Chem. Theory Comput.}, {\bf 2014}, 10, 2194-2203.
+
+\end{thebibliography}
+\endgroup
+
+\newpage
+
+\section{INSTALLATION}
+\label{sect:install}
+
+Please follow the instructions in the installation guide to download and put the package on your
+system. In what follows, \$UNRESROOT is the location of the UNRES package in your system.
+
+It is recommended to install all components of the package using the Cmake utility.
+Please follow the instructions in the installation guide.
+
+This section describes the installation of only the UNRES component of the package,
+using make program. Sample Makefiles are present in the respective source directories.
+
+To produce the executable do the following:
+
+\begin{enumerate}[(a)]
+%a)
+\item
+ To build parallel version, make sure that MPI is installed in your system.
+ Note that the package will have limited functions when compiled in a single-CPU mode.
+ On linux cluster the command source \$HOME/.env should be added to .tcshrc
+ or equivalent file to use parallel version of the program, the
+ alternative is to use queuing system like PBS.
+ In some cases the FORTRAN library subroutine GETENV does not work properly
+ with MPI, if the script is run interactively. In such a case try to
+ add the source mygentenv.F and turn on the -DMYGETENV preprocessor flag.
+%b)
+\item
+ Change directory to the respective source directory.
+%c)
+\item
+ Select the appropriate Makefile\_xxxx or copy the most matching Makefile\_xxx
+ to another name (e.g., Makefile\_MySystem) and edit it to customize to your
+ system. Note that the CSA version works only with MPI.
+
+ Makefile\_pgf90 - Linux, the pgf90 compiler,
+ Makefile\_intel - Linux, Intel Fortran compiler,
+ Makefile\_gfortran - Gnu Fortran compiler,
+ Makefile\_bluegene - BlueGene/Q (AIX Fortan).
+
+\textbf{
+ Please note that Makefile must be a symbolic link to the Makefile\_xxx of choice. Make sure
+that the file cinfo.f is present; if not, execute:
+}
+
+\begin{verbatim}
+touch cinfo.f
+\end{verbatim}
+
+ Other systems should not cause problems; all you have to do is to change
+ the compiler, compiler options, and preprocessor options.
+
+ By default, the executables will be placed in \$UNRESROOT/bin/unres/CSA
+ \$UNRESROOT/bin/unres/MD and UNRES/bin/unres/MINIM, respectively.
+
+ The following architectures are defined in the .F source files:
+
+\begin{description}
+
+ \item{AIX} -- AIX systems (put -DAIX as one of the preprocessor options, if
+ this is your system).
+
+ \item{LINUX} -- Linux (put -DLINUX).
+
+ \item{G77} -- Gnu-Fortran compilers (might require sum moderate source code editing)
+ (put -DG77). The recommended compiler is gfortran and not g77.
+
+ \item{PGI} -- PGI compilers.
+
+ \item{WINPGI} -- additional setting for PGI compilers for MS Windows.
+
+ \item{SGI} -- all SGI platforms; should also be good for SUN platforms (put -DSGI).
+
+ \item{CRAY} -- handles some Cray-specific I/Os and other instructions.
+
+ \item{WIN} -- MS Windows with Digital Fortran compiler (put -DWIN)
+
+\end{description}
+
+ For other platforms, the only problems might appear in connection with
+ machine-specific I/O instructions. Many files are opened in the append
+ mode, whose specification in the OPEN statement is quite machine-dependent.
+ In this case you might need to modify the source code accordingly.
+ The other platform dependent routines are the timing routines contained
+ in timing.F. In addition to the platforms specified above, ES9000, SUN,
+ KSR, and CRAY are defined there.
+
+ For parallel build -DMP and -DMPI must be set (these are set in Makefile).
+
+ IMPORTANT! Apart from this, two define flags: -DCRYST\_TOR and -DMOMENT
+ define earlier versions of the force field. The MUST NOT be entered, if
+ the CASP5 and later versions of the force field are used.
+
+%d)
+\item
+ Build the unres executables by typing at your UNIX prompt:
+
+\begin{verbatim}
+ make # will build unres
+ make clean # will remove the object files
+\end{verbatim}
+
+ The bin directory contains pre-built binaries for Red Hat Linux. These
+ executables are specified in the csh scripts listed in section 4.
+
+%e)
+\item
+ Customize the C-shell scripts unres.unres (to run the parallel version on
+ set of workstation). See the next section of this manual for guidance.
+
+After the executables are build and C-shell scripts customized, you can run the
+test examples contained in UNRES/examples.
+
+\end{enumerate}
+
+\newpage
+
+\section{CUSTOMIZING YOUR C-SHELL SCRIPT}
+\label{sect:custom}
+
+IMPORTANT NOTE -- The unres.csh script is for Linux and should also be easily
+adaptable to other systems running MPICH. This script is for interactive
+parallel jobs. Examples of scripts compatible with PBS (pbs.sub) and LoadLever
+(sp2.sub) queuing systems are also provided.
+
+Edit the following lines in your unres.csh script:
+
+\begin{verbatim}
+set DD = your_database_directory
+\end{verbatim}
+
+e.g., if you installed the package on the directory /usr/local, this line
+looks like this:
+
+\begin{verbatim}
+set DD = /usr/local/UNRES/PARAM
+set BIN = your_binaries_directory
+set FGPROCS = number_of_processors_per_energy/force_evaluation (MD)
+\end{verbatim}
+
+e.g., if the root directory is as above:
+
+\begin{verbatim}
+set BIN = /usr/local/UNRES/bin
+\end{verbatim}
+
+\section{COMMAND LINE AND FILES}
+\label{sect:command}
+
+To run UNRES interactively enter the following command at your Unix prompt
+or put it in the batch script:
+
+\begin{verbatim}
+unres.csh POTENTIAL INPUT N_PROCS
+\end{verbatim}
+
+where:
+
+POTENTIAL specifies the side-chain interaction potential type and must be
+one of the following:
+
+\begin{description}
+
+\item{LJ} -- 6-12 radial Lennard-Jones.
+
+\item{LJK} -- 6-12 radial Lennard-Jones-Kihara (shifted Lennard Jones).
+
+\item{BP} -- 6-12 anisotropic Berne-Pechukas based on Gaussian overlap (dilated
+ Lennard-Jones).
+
+\item{GB} -- 6-12 anisotropic Gay-Berne (shifted Lennard-Jones).
+
+\item{GBV} -- 6-12 anisotropic Gay-Berne-Vorobjev (shifted Lennard-Jones).
+
+See section \ref{sect:forcefields} (Force Fields) for explanation and usage.
+
+At present, only the LJ and GB potentials are applied. The LJ potential
+is used in the ``CASP3'' version of the UNRES force field that is able
+to predict only $\alpha$-helical structures. All further version of the
+UNRES force field use the GB potential. For the description of all above-mentioned
+potentials see ref. \cite{liwo_1997_02}.
+
+\item{INPUT} is the prefix for input and output files (see below)
+
+\item{N\_PROCS} is the number of processors; for a CSA or REMD/MREMD run it MUST be at least 2.
+
+\end{description}
+
+Note! The script takes one more variable, FGPROCS, as the fourth argument,
+which is the number of fine-grain processors to parallelize energy
+evaluations. The corresponding code is in UNRES/CSA, but it was written
+using MPL instead of MPI and therefore is never used in the present version.
+At present we have no plans to rewrite fine-grain parallelization using MPI,
+because we found that the scalability for up to 200 residue polypeptide
+chains was very poor, due to a small number of interactions and,
+correspondingly, unfavorable ratio of the overhead to the computation time.
+
+\begin{description}
+
+\item{INPUT.inp} contains the main input data and the control parameters of the CSA
+ method.
+
+\item{INPUT.out\_POTENTIAL\_xxx} is the main output files from different processors; xxx
+ denotes the number of the processor
+
+\item{INPUT\_POTENTIALxxx.stat} is the summary files with the energies, energy components,
+ and RMS deviations of the conformations produced by each of the processors;
+ not used in CSA runs; also it outputs different quantity in MD/MREMD runs.
+
+CSA version specific files:
+
+\item{INPUT\_POTENTIALxxx.int} is the internal coordinates; in the CSA run
+
+\item{INPUT\_POTENTIAL\_000.int} contains the coordinates of the conformations,
+ and the other files are empty
+
+\item{INPUT.CSA.history} is the history file from a CSA run. This is an I/O file, because
+ it can be used to restart an interrupted CSA run.
+
+\item{INPUT.CSA.seed} stores the random seed generated in a CSA run; written for
+ restart purposes.
+
+\item{INPUT.CSA.bank} is the current bank of conformations obtained in CSA calculations
+ (expressed as internal coordinates). This information is also stored in
+ INPUT\_POTENTIAL000.int
+
+\item{INPUT.CSA.rbank} -- as above, but contains random-generated conformations.
+
+\end{description}
+
+MD version specific files:
+
+\begin{description}
+
+\item{INPUT\_MDyyy.pdb} is the Cartesian coordinates of the conformations in PDB format.
+
+\item{INPUT\_MDyyy.x} is the Cartesian coordinates of the conformations in ASCII format.
+
+\item{INPUT\_MDyyy.cx} is the Cartesian coordinates of the conformations in compressed format
+ (need xdr2pdb to convert to PDB format).
+\end{description}
+
+The program currently produces some more files, but they are not used
+for any purposes and most of them are scratched after a run is completed.
+
+The run script also contains definitions of the parameter files through the
+following environmental variables:
+
+\begin{description}
+
+\item{SIDEPAR} -- parameters of the SC-SC interaction potentials ($U_{SC SC}$);
+
+\item{SCPPAR} -- parameters of the SC-p interaction potential ($U_{SCp}$); this file can
+ be ignored by specifying the -DOLDSCP preprocessor flag, which means that the
+ built-in parameters are used; at present they are the same as the parameters
+ in the file specified by SCPPAR;
+
+\item{ELEPAR} -- parameters of the p-p interaction potentials ($U_{pp}$);
+
+\item{FOURIER} -- parameters of the multibody potentials of the coupling between the
+ backbone-local and backbone-electrostatic interactions ($U_{corr}$);
+
+\item{THETPAR} -- parameters of the virtual-bond-angle bending potentials ($U_b$);
+
+\item{ROTPAR} -- parameters of the side-chain rotamer potentials ($U_{rot}$);
+
+\item{TORPAR} -- parameters of the torsional potentials ($U_{rot}$);
+
+\item{TORDPAR} -- parameters of the double-torsional potentials.
+
+\item{SCCORPAR} -- parameters of the torsional potentials that account for the
+coupling between the local backbone and local sidechain states (implemented recently).
+
+\end{description}
+
+\newpage
+
+\section{FORCE FIELDS}
+\label{sect:forcefields}
+
+UNRES is being developed since 1997 and several versions of the force field
+were produced. The settings and references to these force fields are
+summarized below.
+
+Force fields for CSA version (can be used in MD but haven't been parameterized for this
+purpose).
+
+{\small
+\hspace{-2cm}\begin{longtable}{|l|l|l|l|l|l|l|}\hline
+\small
+%---------------------------------------------------------------------------------------
+ & Additional & SC-SC & Example script & Structural &\\
+Force field & compiler flags& potential& and executables & classes covered& References\\
+ & & & (Linux; PGF90 &&\\
+ & & & and IFC) &&\\ \hline
+%---------------------------------------------------------------------------------------
+CASP3 & -DCRYST\_TOR & LJ & unres\_CASP3.csh &only $\alpha$ &\cite{liwo_1997,liwo_1997_02,liwo_1998}\\
+ & -DCRYST\_BOND & &unres\_pgf90\_cryst\_tor.exe&&\\
+ & -DCRYST\_THETA & &unres\_ifc6\_cryst\_tor.exe &&\\
+ & -DCRYST\_SC &&&&\\
+ & -DMOMENT &&&&\\
+&&&&&\\
+ALPHA & -DMOMENT & GB & unres\_CASP4.csh &only $\alpha$ &\cite{liwo_2001,lee_2001,pillardy_2001}\\
+ & -DCRYST\_BOND & &unres\_pgf90\_moment.exe &&\\
+ & -DCRYST\_THETA & &unres\_ifc6\_moment.exe &&\\
+ & -DCRYST\_SC &&&&\\
+&&&&&\\
+BETA & -DMOMENT & GB & unres\_CASP4.csh &only $\beta$ &\cite{liwo_2001,lee_2001,pillardy_2001}\\
+ & -DCRYST\_BOND & &unres\_pgf90\_moment.exe &&\\
+ & -DCRYST\_THETA & &unres\_ifc6\_moment.exe &&\\
+ & -DCRYST\_SC&&&&\\
+&&&&&\\
+ALPHABETA & -DMOMENT & GB & unres\_CASP4.csh & all &\cite{liwo_2001,lee_2001,pillardy_2001}\\
+ & -DCRYST\_BOND & &unres\_pgf90\_moment.exe &&\\
+ & -DCRYST\_THETA & &unres\_ifc6\_moment.exe &&\\
+ & -DCRYST\_SC &&&&\\
+&&&&&\\
+CASP5 & -DCRYST\_BOND & GB & unres\_CASP5.csh & all &\cite{liwo_2002,saunders_2003,saunders_2003_02,liwo_2004}\\
+ & -DCRYST\_THETA & & unres\_pgf90.exe &&\\
+ & -DCRYST\_SC & & unres\_ifc6.exe &&\\
+&&&&&\\
+3P & -DCRYST\_BOND & GB & unres\_3P.csh & all &\cite{oldziej_2004,oldziej_2004_02}\\
+ & -DCRYST\_THETA & & unres\_pgf90.exe &&\\
+ & -DCRYST\_SC & & unres\_ifc6.exe &&\\
+&&&&&\\
+4P & -DCRYST\_BOND & GB & unees\_4P.csh & all &\cite{oldziej_2004,oldziej_2004_02}\\
+ & -DCRYST\_THETA & & unres\_pgf90.exe&&\\
+ & -DCRYST\_SC & & unres\_ifc6.exe&&\\ \hline
+%---------------------------------------------------------------------------------------
+\end{longtable}
+}
+
+\newpage
+
+Force fields for MD version \cite{khalili_2005,khalili_2005_02}.
+
+{\small
+\begin{longtable}{|l|l|l|l|l|l|l|}\hline
+%---------------------------------------------------------------------------------------
+ & Additional & SC-SC & Example script & Structural &\\
+Force field & compiler flags& potential& and executables & classes covered& References\\
+ & & & (Linux; PGF90&&\\
+ & & & and IFC)&&\\ \hline
+%---------------------------------------------------------------------------------------
+GAB & -DCRYST\_BOND & GB & unres\_GAB.csh & mostly $\alpha$ & \cite{liwo_2007}\\
+ & -DCRYST\_THETA &&&&\\
+ & -DCRYST\_SC &&&&\\
+ & -DPROCOR &&&&\\
+&&&&&\\
+E0G & -DCRYST\_BOND & GB & unres\_E0G.csh & mostly $\alpha$ & \cite{liwo_2007}\\
+ & -DCRYST\_THET &&&&\\
+ & -DCRYST\_SC &&&&\\
+ & -DPROCOR &&&&\\
+&&&&&\\
+E0LL2Y &-DPROCOR & GB & unres\_ab.csh & all & \cite{liwo_2007,kozlowska_2007,he_2009,kozlowska_2010,kozlowska_2010_02}\\ \hline
+%---------------------------------------------------------------------------------------
+\end{longtable}
+}
+
+The example scripts (the *.csh filed) contain all appropriate parameter files, while
+the energy-term weights are provided in the example input files listed in EXAMPLES.TXT
+(*.inp; see section \ref{sect:input}. for description of the input files). However, it is user's
+responsibility to specify appropriate compiler flags. Note that a version WILL NOT work,
+if the force-field specific compiler flags are not set. The parameter files specified
+in the run script also must strictly correspond to the energy-term weights specified in
+the input file. The parameter files for specific force fields are also specified below
+and the energy-term weights are specified in section \ref{sect:input}.
+
+The parameter files are as follows (the environment variables from section \ref{sect:command} are
+used to identify the parameters):
+
+CASP3:
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm \\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_cryst.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm (not used)\\
+SIDEPAR &scinter\_LJ.parm\\
+ELEPAR &electr.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_GAP.parm (not used)\\
+SCCORPAR&sccor\_am1\_pawel.dat (not used)\\
+\end{longtable}
+
+ALPHA, BETA, ALPHABETA (CASP4):
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm \\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_ecepp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm (not used)\\
+SIDEPAR &scinter\_GB.parm\\
+ELEPAR &electr.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_GAP.parm\\
+SCCORPAR&sccor\_am1\_pawel.dat (not used)\\
+\end{longtable}
+
+CASP5:
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm\\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_631Gdp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm\\
+SIDEPAR &scinter\_GB.parm\\
+ELEPAR &electr\_631Gdp.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_opt.parm.1igd\_iter7n\_c\\
+SCCORPAR&sccor\_am1\_pawel.dat (not used)\\
+\end{longtable}
+
+3P:
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm\\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_631Gdp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm\\
+SIDEPAR &sc\_GB\_opt.3P7\_iter81\_1r\\
+ELEPAR &electr\_631Gdp.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
+SCCORPAR&sccor\_am1\_pawel.dat (not used)\\
+\end{longtable}
+
+4P:
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm\\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_631Gdp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm\\
+SIDEPAR &sc\_GB\_opt.4P5\_iter33\_3r\\
+ELEPAR &electr\_631Gdp.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
+SCCORPAR&sccor\_am1\_pawel.dat (not used)\\
+\end{longtable}
+
+GAB:
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm\\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_631Gdp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm\\
+SIDEPAR &sc\_GB\_opt.1gab\_3S\_qclass5no310-shan2-sc-16-10-8k\\
+ELEPAR &electr\_631Gdp.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
+SCCORPAR&sccor\_pdb\_shelly.dat\\
+\end{longtable}
+
+E0G:
+
+\begin{longtable}{ll}
+BONDPAR &bond.parm\\
+THETPAR &thetaml.5parm\\
+ROTPAR &scgauss.parm\\
+TORPAR &torsion\_631Gdp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm\\
+SIDEPAR &sc\_GB\_opt.1e0g-52-17k-2k-newclass-shan1e9\_gap8g-sc\\
+ELEPAR &electr\_631Gdp.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
+SCCORPAR&sccor\_pdb\_shelly.dat\\
+\end{longtable}
+
+E0LL2Y:
+
+\begin{longtable}{ll}
+BONDPAR &bond\_AM1.parm\\
+THETPAR &theta\_abinitio.parm\\
+ROTPAR &rotamers\_AM1\_aura.10022007.parm\\
+TORPAR &torsion\_631Gdp.parm\\
+TORDPAR &torsion\_double\_631Gdp.parm\\
+SIDEPAR &scinter\_\${POT}.parm\\
+ELEPAR &electr\_631Gdp.parm\\
+SCPPAR &scp.parm\\
+FOURIER &fourier\_opt.parm.1igd\_hc\_iter3\_3\\
+SCCORPAR&sccor\_am1\_pawel.dat\\
+\end{longtable}
+
+Additionally, for E0LL2Y, the following environment variables and files are required
+to generate random conformations:
+
+THETPARPDB thetaml.5parm\\
+ROTPARPDB scgauss.parm
+
+For CSA, the best force field is 4P. For MD, the 1L2Y\_1LE1 force field is best for
+ab initio prediction but provides medium resolution (5 A for 60-residue proteins) and
+overemphasizes $\beta$-structures and has to be run with secondary-structure-prediction
+information. For prediction of the structure of mostly $\alpha$-protein, and for running
+dynamics of large proteins, the best is the GAB force field. All these force fields
+were trained by using our procedure of hierarchical optimization \cite{oldziej_2004,oldziej_2004_02}.
+The 4P and 1L2Y\_1LE1 force fields have considerable power independent of structural class.
+The ALPHA, BETA, and ALPHABETA force fields (for CSA) were used in the CASP4 exercises
+and the CASP5 force field was used in the CASP5 exercise with some success; ALPHA
+predicts reasonably the structure of $\alpha$-helical proteins and is still not obsolete,
+while for $\beta$- and $\alpha+\beta$-structure prediction
+3P or 4P should be used, because they are cheaper and more reliable than BETA and
+ALPHABETA. The early CASP3 force field is included for historical reasons only.
+
+\newpage
+
+\section{INPUT FILES}
+\label{sect:input}
+
+\subsection{Main input data file}
+\label{sect:input:main}
+
+Most of the data are organized as data lists, where the data can be put
+in any order, using a series of statements of the form:
+
+KEYWORD=value
+
+for simple non-logical variables
+
+or just
+
+KEYWORD
+
+to indicate that the corresponding option is turned on. For array variables
+the assignment statement is:
+
+KEYWORD=value1,value2,...
+
+However, the data lists are unnamed and that must be placed EXACTLY in the
+order indicated below. The presence of an \& in the 80th column of a line
+indicates that the next line will belong to the same data group. The parser
+subroutines that interpret the keywords are case insensitive.
+
+Each group of data organized as a data list is indicated as data list format
+input.
+
+\subsubsection{Title}
+\label{sect:input:main:title}
+
+Any string containing up to 80 characters. The first input line is always
+interpreted as title.
+
+\subsubsection{Control data}
+\label{sect:input:main:control}
+
+This data section is in data list format and is read in the READ\_CONTROL subroutine.
+
+\paragraph{Keywords to chose calculation type}
+
+\begin{description}
+
+\item{TIMLIM} -- time limit in minutes (960)
+
+%\item{OUT1FILE} -- only the master processor prints the output file in a parallel job
+
+\item{MINIMIZE} -- if present, energy minimization will be carried out.
+
+\item{REGULAR} -- regularize the read in conformation (usually a crystal or
+ NMR structure) by doing a series of three constrained minimizations,
+ to keep the structure as close as possible to the starting
+ (experimental) structure. The constraints are the CA-CA distances
+ of the initial structure. The constraints are gradually diminished
+ and removed in the last minimization.
+
+\item{SOFTREG} -- regularize the read in conformation (usually a crystal or NMR
+ structure) by doing a series of constrained minimizations, with
+ additional use of soft potential and secondary structure
+ freezing, to keep the structure as close as possible to the
+ starting (experimental) structure.
+
+
+\item{CSA} -- if present, the run is a CSA run. At present, this is the only
+ reliable mode of doing global conformational search with this
+ package; it is NOT recommended to use MCM or THREAD for this
+ purpose.
+
+\item{MCM} -- if present, this is a Monte Carlo Minimization (MCM) run.
+
+\item{MULTCONF} -- if present, conformations will be read from the INPUT.intin
+ file.
+
+\item{MD} -- run canonical MD (single or multiple trajectories).
+
+\item{RE} -- run REMD or MREMD (parallel jobs only).
+
+\item{MUCA} -- run multicanonical MD calculations (parallel jobs only).
+
+\item{MAP=number} (integer) --
+Conformational map will be calculated in chosen angles.
+
+\item{THREAD=number} (integer) --
+Threading or threading-with-minimization run, using a database of structures
+contained in the \$DD/patterns.cart pattern data base (502 chains or chain
+fragments), using a total number patterns. It is recommended to use this with
+energy minimization; this implies regularization of each minimized pattern.
+See refs. \cite{liwo_1997_02} and \cite{liwo_1997_03}.
+
+\item{CHECKGRAD} -- compare numerical and analytical gradient; to be followed by:
+
+\item{CART} -- energy gradient in virtual-bond vectors (Cartesian coordinates)
+
+\item{INT} -- energy gradient in internal coordinates (default)
+
+\item{CARINT} -- derivatives of the internal coordinates in the virtual-bond vectors.
+
+\end{description}
+
+\paragraph{Specification of protein and structure output in non-MD applications}
+
+\begin{description}
+
+\item{ONE\_LETTER} -- one-letter and not three-letter code of the amino-acid residues
+ is used.
+
+\item{SYM} (1) -- number of chains with same sequence (for oligomeric proteins only).
+
+\item{PDBSTART} -- the initial conformation is read in from a PDB file.
+
+\item{UNRES\_PDB} -- the starting conformation is in UNRES representation (C$^\alpha$
+ and SC coordinates only). This keyword MUST appear in such a case
+ or the program will generate erroneous and unrealistic side-chain
+ coordinates.
+
+\item{RAND\_CONF} -- start from a random conformation.
+
+\item{EXTCONF} -- start from an extended chain conformation.
+
+\item{PDBOUT} -- if present, conformations will be output in PDB format. Note that
+ this keyword affects only the output from single energy evaluation,
+ energy minimization and multiple-conformation data. To request
+ conformations from MD/MREMD runs in PDB format, the MDPDB keyword
+ must be placed on the MD input record.
+
+\item{MOL2OUT} -- if present, conformations will be output in SYBYL mol2 format.
+
+\item{REFSTR} -- if present, reference structure will be read (e.g., to monitor
+ the RMS deviation from the crystal structure).
+
+\item{PDBREF} -- if present, a reference structure will be read in to compare
+ the calculated conformations with it.
+
+\item{UNRES\_PBD} -- the starting/reference structure is read from an UNRES-generated
+ PDB file.
+
+\end{description}
+
+Keywords: PDBOUT, MOL2OUT, PDBREF, and PDBSTART are ignored for a CSA run.
+Output mode for MD version is specified in MD input (see section \ref{sect:input:main:MD}).
+
+\paragraph{Miscellaneous}
+
+\begin{description}
+
+\item{CONSTR\_DIST=number}
+
+\begin{description}
+\item{0} -- no distance restraints,
+\item{$>0$} -- imposes harmonic restraints on selected distances; see section 5.12.
+In MD version, also restraints on the q variable \cite{liwo_2007} can be used.
+\end{description}
+
+\item{WEIDIS=number} (real)
+the weight of the distance term; applies for REGULARIZE and THREAD, otherwise
+ignored.
+
+\item{USE\_SEC\_PRED} -- use secondary-structure prediction information.
+
+\item{SEED=number} (integer) (no default)
+Random seed (required, even if the run is not a CSA, MCM, MD or MREMD run).
+
+\item{PHI} -- only the virtual-bond dihedral angles $\gamma$ are considered as
+ variables in energy minimization.
+
+\item{BACK} -- only the backbone virtual angles (virtual-bond angles theta and
+ virtual-bond dihedral angles $\gamma$) are considered as variables
+ in energy minimization.
+
+By default, all internal coordinates: $\theta$, $\gamma$, and the side-chain
+centroid polar angles $\alpha$ and $\beta$ are considered as variables in energy
+minimization.
+
+\item{RESCALE\_MODE=number} (real)
+Choice of the type of temperature dependence of the force field.
+\begin{description}
+\item{0} -- no temperature dependence
+\item{1} -- homographic dependence (not implemented yet with any force field)
+\item{2} -- hyperbolic tangent dependence \cite{liwo_2007}.
+\end{description}
+
+\item{T\_BATH=number} (real)
+temperature (for MD runs and temperature-dependent force fields).
+\end{description}
+
+The following keywords apply to MCM only:
+
+\begin{description}
+
+\item{MAXGEN=number} (integer) (10000)
+maximum number of conformations generated in a single MCM iteration
+
+\item{MAXOVERLAP=number} (integer) (1000)
+maximum number of conformations with ``bad'' overlaps allowed to appear in a
+row in a single MCM iteration.
+
+\item{DISTCHAINMAX} -- (multi-chain capacity only) maximum distance between the
+ last residue of a given chain and the first residue of the
+ next chain such that restraints will not be imposed; quartic
+ restraints will be imposed for greater distances.
+
+\item{ENERGY\_DEC} -- detailed energies will be printed for each interacting pair
+ or each virtual bond, virtual-bond angle and dihedral angle,
+ side chain, etc. DO NOT use unless a single energy evaluation
+ was requested.
+\end{description}
+
+\subsubsection{Minimizer options}
+
+This data section is in data list format and is read in the READ\_MINIM subroutine.
+
+This data group is present, if MINIMIZE was specified on the control card.
+Otherwise, it must not appear.
+
+\begin{description}
+
+\item{CART} -- minimize in virtual-bond vectors instead of angles.
+
+\item{MAXMIN=number} (integer) (2000)
+maximum number of iterations of the SUMSL minimizer.
+
+\item{MAXFUN=number} (integer) (5000)
+maximum number of function evaluations in a single minimization.
+
+\item{TOLF=number} (real) (1.0e-2)
+Tolerance on function.
+
+\item{RTOLF=number} (real) (1.0d-4)
+Relative tolerance on function.
+
+\item{PRINT\_INI} -- turns on printing nondefault minimization parameters,
+initial variables, and gradients in the SUMSL procedures.
+
+\item{PRINT\_FINAL} -- turns on printing final variables and gradients in
+SUMSL.
+
+\item{PRINT\_STAT} -- turns on printing abbreviated minimization protocol.
+
+\end{description}
+
+The SUMSL minimizer is used in UNRES/CSA. For detailed description of
+the control parameters see the source file cored.f and sumsld.f
+
+
+\subsubsection{CSA control parameters}
+\label{sect:input:main:CSA}
+
+This data group should be present only, if CSA was specified on the control
+card. It is recommended that the readers to read publications on CSA method
+for more complete description of the parameters. Brief description of
+parameters:
+
+\begin{description}
+
+\item{NCONF=number} (integer) (50)
+This corresponds to the size of the bank at the beginning of the
+CSA procedure. The size of the bank, nbank, is set to nconf.
+If necessary (at much later stages of the CSA: see icmax below),
+nbank increases by multiple of nconf.
+
+\item{JSTART=number} (integer) (1)
+
+\item{JEND}=number (integer) (1)
+This corresponds to the limit values of do loop, each of which
+corresponds to an separate CSA run. If jstart=1, and jstart=100,
+this routine will repeat 100 separate CSA runs (limited by CPU)
+each one with separate random number initialization.
+The only difference between two CSA runs (one with jstart=jend=1
+and another one with jstart=jend=2) would be different random
+number initializations if other parameters are identical.
+
+\item{NSTMAX=number} (integer) (500000)
+This is to set a limit the total number of local minimizations of CSA
+before termination.
+
+\end{description}
+
+N1=number (integer) (6)\\
+N2=number (integer) (4)\\
+N3=number (integer) (0)\\
+N4=number (integer) (0)\\
+N5=number (integer) (0)\\
+N6=number (integer) (10)\\
+N7=number (integer) (0)\\
+N8=number (integer) (0)\\
+N9=number (integer) (0)\\
+IS1=number (integer) (1)\\
+IS2=number (integer) (8)\\
+
+These numbers are used to generate trial conformations for each seed.
+See the file newconf.f for more details.
+
+\begin{description}
+ \item{n1:} the total number of trial conformations for each seed by substituting
+ nran number of variable angles (see subroutine newconf1ab and
+ subroutine newconf1ar),
+ \item{n2:} the total number of trial conformations for each seed by substituting
+ nran number of groups of variable angles (see subroutine newconf1bb and
+ subroutine newconf1br),
+ \item{n3:} the total number of trial conformations for each seed by substituting
+ a window of residues which forms a $\beta$-hairpin, if there is no enough
+ $\beta$-hairpins uses the same algorithm as n6,
+ \item{n4:} the total number of trial conformations for each seed by shifting the
+ turn in $\beta$-hairpin by +/- 1 or 2 residues, if there is no enough
+ $\beta$-hairpins uses the same algorithm as n6,
+ \item{n5:} not used,
+ \item{n6:} the total number of trial conformations for each seed by substituting
+ a window of residues [is1,is2] inclusive. The size of the window is
+ determined in a random fashion (see subroutine newconf\_residue for
+ generation of the trial conformations),
+ \item{n7:} the total number of trial conformations for each seed by copying a
+ remote strand pair forming nonlocal $\beta$-sheet contact,
+ \item{n8:} the total number of trial conformations for each seed by copying an
+ $\alpha$-helical segment,
+ \item{n9:} the total number of trial conformations for each seed by shifting the
+ $\alpha$-helical segment by +/- 1 or 2 residues.
+\end{description}
+
+Typical values used for a 75-residue helical protein is
+(6 4 0 0 0 10 1 26) for (n1,n2,n3,n4,n5,n6,is1,is2), respectively.
+In this example, a total of 20 trial conformations are generated for a seed
+Usually is1=1 is used for all applications, and the value of is2 is set about
+to 1/3 of the total number of residues. n3, n4 and n7 are design to help in
+case of proteins with $\beta$-sheets
+
+NRAN0=number (integer) (4)\\
+NRAN1=number (integer) (2)\\
+IRR=number (integer) (1)\\
+
+These numbers are used to determine if the CSA stage is very early.
+One can use (4 2 1) for these values. For more details one should look into
+the file, newconf.f, for more details.
+
+NTOTAL=number (integer) (10000)\\
+CUT1=number (real) (2.0)\\
+CUT2=number (real) (5.0)\\
+
+Annealing schedule is set in following fashion.
+The value of D\_cut is reduced geometrically from 1/cut1 of D\_ave (at the
+beginning) to 1/cut2 of D\_ave (after ntotal number of minimizations) where
+D\_ave is the average distance between two conformations in the First\_bank.
+
+\begin{description}
+
+\item{ESTOP=number} (real) (-3000.0)
+The CSA procedure stops if a conformations with energy lower than estop is
+obtained. If the do-loop set by jstart and jend requires more than one loop,
+the program will go on until the do-loop is finished.
+
+\item{ICMAX=number} (integer) (3)
+The maximum value of cycle (see the original publications for details).
+If the number of cycle exceeds this value the program will add nconf
+more conformations to Bank and First\_bank to continue CSA procedure if
+the new size of the nbank is within the maximum set by nbankm (see above).
+If the size of nbank exceeds the maximum set by nbankm the CSA procedure
+for this run will stop and next CSA will begin depending on the do-loop
+set by jstart and jend.
+
+\item{IRESTART=number} (integer) (0)
+This tells you if the run is fresh start (irestart=0) or a restart (irestart=1)
+starting from an old results
+
+\item{NDIFF=number} (integer) (2)
+The number of variables use in comparison when structure is added to the
+bank,4 - all angels, 2 - only backbone angles $\gamma$ and $\theta$
+
+\item{NBANKTM=number} (integer) (0)
+The maximum number of structures saved in *.CSA.bankt as history of the run
+Do not use bankt on massively parallel computation as it kills scalability.
+
+\item{DELE=number} (real) (20.0)
+Energy cutoff for bankt.
+
+\item{DIFCUT=number} (real) (720.0)
+Angle cutoff for bankt.
+
+\item{IREF=number} (integer) (0)
+0 - normal run, 1 - local CSA which generates only structures close to the
+reference one read from *.CSA.native.int file.
+
+\item{RMSCUT=number} (real) (4.0)
+CA RMSD cut off used in local CSA
+
+\item{PNCCUT=number} (real) (0.5)
+Percentage of native contact used in local CSA
+
+\item{NCONF\_IN=number} (integer) (0)
+The number of conformation read for the first bank from the input file
+*.intin
+\end{description}
+
+Optionally, the CSA parameters can be read from file INPUT.CSA.in, if
+this file exists. If so, they are read in free format in the following
+order:
+
+nconf\\
+jstart,jend\\
+nstmax\\
+n1,n2,n3,n4,n5,n6,n7,n8,is1,is2\\
+nran0,nran1,irr\\
+nseed\\
+ntotal,cut1,cut2\\
+estop\\
+icmax,irestart\\
+ntbankm,dele,difcut\\
+iref,rmscut,pnccut\\
+ndiff\\
+
+
+\subsubsection{MCM data}
+\label{sect:input:main:MCM}
+
+(Data list format, subroutine MCMREAD.)
+
+This data group is present, if MCM was specified on the control card.
+Otherwise it must not appear.
+
+\begin{description}
+
+\item{MAXACC=number} (integer) (100)
+Maximum number of accepted conformations.
+
+\item{MAXTRIAL=number} (integer) (100)
+Maximum number of unsuccessful trials in a row.
+
+\item{MAXTRIAL\_ITER=number} (integer) (1000)
+Maximum number of unsuccessful trials in a single iteration.
+
+\item{MAXREPM=number} (integer) (200)
+Maximum number of repetitions of the same minimum.
+
+\item{RANFRACT=number} (real) (0.5d0)
+Fraction of chain-rebuild motions.
+
+\item{OVERLAP=number} (real) (1.0d3)
+Bad contact energy criterion.
+
+\item{NSTEPH=number} (integer) (0)
+Number of heating step in adaptive sampling.
+
+\item{NSTEPC=number} (integer) (0)
+Number of cooling step in adaptive sampling.
+
+\item{TMIN=number} (real) (298.0d0)
+Minimum temperature in adaptive-temperature sampling).
+
+\item{TMAX=number} (real) (298.0d0)
+Maximum temperature in adaptive-temperature sampling).
+
+The temperature is changed according to the formula:
+
+T = TMIN*EXP(ISTEPH*(TMAX-TMIN)/NSTEPH) when heating
+
+and
+
+T = TMAX*EXP(-ISTEPC*(TMAX-TMIN)/NSTEPC) when cooling
+
+The default is to use a constant temperature.
+
+\item{NWINDOW=number} (integer) (0)
+Number of windows in which the variables will be perturbed; the windows are
+defined by the numbers of the respective amino-acid residues. If NWINDOW
+is nonzero, after specifying all MCM input the next lines must define the
+windows. Each line looks like this:
+
+winstart winend (free format)
+
+e.g. if NWINDOW=2, the input:
+
+4 10\\
+15 20\\
+
+will mean that only the variables of residues 4-10 and 15-20 will be perturbed.
+However, in general, all variables will be considered in minimization.
+
+\item{PRINT\_MC=number} (0)
+Printout level in MCM. 0 - no intermediate printing, 1 and 2 - moderate
+printing, 3 - extensive printing.
+
+\item{NO\_PRINT\_STAT} -- no output to INPUT\_POTENTIALxxx.stat.
+
+\item{NO\_PRINT\_INT} -- no internal-coordinate output to INPUT\_POTENTIALxxx.int.
+
+\end{description}
+
+\subsubsection{MD data}
+\label{sect:input:main:MD}
+
+(Mixed format; subroutine READ\_MDPAR.)
+
+\begin{description}
+
+\item{NSTEP} (1000000) number of time steps per trajectory.
+
+\item{NTWE} (100) NTWX (1000) frequency of energy and coordinate output, respectively.
+The coordinates are dumped in the pdb or compressed Gromacs (cx) format,
+depending on the next keyword.
+NTWE=0 means no energy dump.
+
+\item{MDPDB} - dump coordinates in the PDB format (cx otherwise)
+
+\item{TRAJ1FILE} only the master processor outputs coordinates. This feature pertains
+ only to REMD/MREMD jobs and overrides NTWX; coordinates are dumped at every
+ exchange in MREMD.
+
+\item{REST1FILE} only the master writes the restart file
+
+\item{DT} (real) (0.1) time step; the unit is ``molecular time unit'' (mtu); 1 mtu = 48.9 fs
+
+\item{DAMAX} (real) (1.0) maximum allowed change of acceleration during a single time step.
+The time step gets scaled down, if this is exceeded.
+
+\item{DVMAX} (real) (20.0) -- maximum allowed velocity (in A/mtu)
+
+\item{EDRIFTMAX} (real) (10.0) -- maximum allowed energy drift in a single MD step (10 kcal/mol)
+
+\item{REST} -- restart flag. The calculation is restarted if present.
+
+\item{LARGE} -- very detailed output. Don't use except for debugging.
+
+\item{PRINT\_COMPON} -- prints energy components.
+
+\item{RESET\_MOMENT} (1000) -- frequency of zeroing out the total angular momentum when
+running Berendsen mode calculations (for Langevin calculations meaningless).
+
+\item{RESET\_VEL}=number (integer) (1000) -- frequency of resetting velocities to values
+from Gaussian distribution.
+
+\item{RATTLE} -- use the RATTLE algorithm (constraint bonds); not yet implemented.
+
+\item{RESPA} -- use the Multiple Time Step (MTS) or Adaptive Multiple Time Step (A-MTS)
+algorithm \cite{rakowski_2006}. Without this flag the variable time step (VTS) \cite{khalili_2005} is run.
+
+\item{NTIME\_SPLIT=number} (integer) (1) -- initial number of time-split steps
+
+\item{MAXTIME\_SPLIT=number} (integer) (64) -- maximum number of time-split step
+
+If NTIME\_SPLIT==MAXTIME\_SPLIT, MTS is run.
+
+\item{R\_CUT=number} (real) (2.0) -- the cut-off distance in splitting the forces into short- and
+long-range in site-site VDW distance units.
+
+\item{LAMBDA} (real) (0.3) -- the transition length (in site-site VDW distance units) between
+short- and long-range forces.
+
+\item{XIRESP} -- flag to use MTS/A-MTS with Nos\'e-Hoover/Nos\'e-Poincar\'e thermostats.
+
+\item{LANG=number} (integer) (0) Langevin dynamics flag:
+
+\begin{description}
+\item{0} -- No explicit Langevin dynamics.
+\item{1} -- Langevin with direct integration of the equations of motion (recommended
+ for Langevin calculations)
+\item{2} -- Langevin calculation with analytical pre-integration of the friction and
+ stochastic part of the equations of motion using an algorithm adapted from TINKER.
+ This is MUCH MORE time- and memory-consuming than 1 and requires compiling without
+ the -DLANG0 flag and enormously increases memory requirements.
+\item{3} -- The stochastic integrator developed by Cicotti and coworkers.
+\item{4} -- for other stochastic integrators (not used at present).
+\end{description}
+
+Note: With the enclosed code, the -DLANG0 compiler flag is included which disables
+LANG=2 and LANG=3
+
+\item{TBF} -- Berendsen thermostat.
+
+\item{TAU\_BATH} (1.0) (units are mtus; 1mtu=48.9 fs) -- constant of the coupling to the thermal bath
+ used with the Berendsen thermostat.
+
+\item{NOSEPOINCARE99} -- the Nose-Poincare thermostat as of 1999 will be used.
+
+\item{NOSEPOINCARE01} -- the Nose-Poincare thermostat as of 2001 will be used.
+
+\item{NOSEHOOVER96} -- the Nose-Hoover thermostat will be used.
+
+\item{Q\_NP=number} (real) (0.1) -- the value of the mass of the fictitious particle in the calculations
+ with the Nose-Poincare thermostat.
+
+\item{T\_BATH} (300.0) (in K) -- temperature of canonical simulation or temperature to generate
+velocities.
+
+\item{ETAWAT} (0.8904) -- viscosity of water (in centipoises).
+
+\item{RWAT} (1.4) -- radius of water molecule (in A)
+
+\item{SCAL\_FRIC=number} (real) (0.02) -- scaling factor of the friction coefficients.
+
+\item{SURFAREA} -- scale friction acting on atoms by atoms' solvent accessible area.
+
+\item{RESET\_FRICMAT=number} (integer) (1000) -- recalculate friction matrix every RESET\_FRICMAT MD steps.
+
+\item{USAMPL} -- restraints on q (see reference 5 for meaning) will be imposed (see section .
+In this case, the next records specify the restraints; these records are
+placed before the list of temperatures or numbers of trajectories.
+
+\item{EQ\_TIME=number} (real) (1.0e4) -- time (in mtus; 1 mtu=48.9 fs) after which restraints
+on q will start to be in force.
+
+\end{description}
+
+If USAMPL has been specified, the following information must be supplied after the
+main MD input data record (subroutine READ\_FRAGMENTS):
+
+Line 1: nset, npair, nfrag\_back (number of sets of restraints, number of restrained
+fragments, number of restrained pairs, number of restrained backbone fragments
+(in terms of $\theta$ and $\gamma$ angles)
+
+For each set of restraints (1, 2,..., nset):
+
+\begin{description}
+
+\item{mset(iset)} -- how many times the set is multiplied.
+
+\item{wfrag(i,iset), ifrag(1,i,iset), ifrag2(2,i,iset),qfrag(i,iset)} --
+weight of the restraint, first and last residue of the fragment, target q value.
+This information is repeated through nfrag.
+
+\item{wpair(i,iset), ipair(1,i,iset), ipair(2,i,iset),qinpair(i,iset)} --
+weight of the restraint, first and second fragment of the pair (according to fragment
+list), target q value. This information is repeated through npair
+
+\item{wfrag\_back(1,i,iset), wfrag\_back(2,i,iset), wfrag\_back(3,i,iset),
+ifrag\_back(1,i,iset),ifrag\_back(2,i,iset)} --
+weight of the restraints on $\theta$ angles, weight on the restraints on $\gamma$ angles,
+weight of the restraints on side-chain rotamers, first residue of the fragment,
+last residue of the fragment. This information is repeated through nfrag\_back.
+
+\end{description}
+
+\subsubsection{REMD/MREMD data}
+label{sect:input:main:MREMD}
+
+(Miced format; subroutine READ\_REMDPAR.)
+
+\begin{description}
+
+\item{NREP} (3) -- number of replicas in a REMD/MREMD run.
+
+\item{NSTEX} (1000) -- number of steps after which exchange is performed in REMD/MREMD
+ runs.
+
+The temperatures in replicas can be specified through
+
+\item{RETMIN} (10.0) -- minimum temperature in a REMD/MREMD run,
+
+\item{RETMAX} (1000.0) -- maximum temperature in a REMD/MREMD run.
+
+\end{description}
+
+Then the range from retmin to retmax is divided into equal segments and
+temperature of the replicas assigned accordingly,
+
+or
+
+\begin{description}
+
+\item{TLIST} means that the NREP temperature of the replicas will be input in the
+next record.
+
+\item{MLIST} numbers of trajectories per each of the NREP temperatures will be
+specified in the record after the list of temperatures; this specifies
+a MREMD run.
+
+\end{description}
+
+Important! The number of processors must be exactly equal to the number of
+trajectories, i.e., NREP for a REMD run or $\sum_i mlist(i)$ for a MREMD run.
+
+\begin{description}
+
+\item{SYNC} -- all trajectories will be synchronized every NSTEX time steps
+(by default, they are not synchronized).
+
+\item{TRAJ1FILE} -- only the master processor outputs coordinates. This feature pertains
+ only to REMD/MREMD jobs and overrides NTWX; coordinates are dumped at every
+ exchange in MREMD.
+
+\item{REST1FILE} -- only the master writes the restart file.
+
+\item{HREMD} -- Hamiltonian replica exchange flag; not only temperatures but also
+sets energy-term weights are exchanged between conformations.
+
+\item{TONLY} -- run a ``fake'' HREMD with many sets of energy-term weights in a
+single run but only temperature exchange.
+
+\end{description}
+
+\subsubsection{Energy-term weights}
+\label{sect:input:main:weights}
+
+(Data list format; subroutine MOLREAD.)
+
+\begin{description}
+
+\item{WLONG=number} (real) (1.0d0) --
+common weight of the U(SC-SC) (side-chain side-chain interaction)
+and U(SC,p) (side-chain peptide-group) term.
+
+\item{WSCC=number} (real) (WLONG) --
+weight of the U(SC-SC) term.
+
+\item{WSCP=number} (real) (WLONG)
+weight of the U(SC-p) term.
+
+\item{WELEC=number} (real) (1.0d0)
+weight of the U(p-p) (peptide-group peptide-group interaction) term.
+
+\item{WEL\_LOC=number} (real) (1.0d0)
+weight of the $U_{el;loc}^3$ (local-electrostatic cooperativity, third-order) term.
+
+\item{WCORRH=number} (real) (1.0d0)
+weight of the U(corr) (cooperativity of hydrogen-bonding interactions, fourth-order) term.
+
+\item{WCORR5=number} (real) (0.0d0) --
+weight of the $U_{el;loc}^5$ (local-electrostatic cooperativity, 5th order
+contributions).
+
+\item{WCORR6=number} (real) (0.0d0) --
+weight of the $U_{el;loc}^6$ (local-electrostatic cooperativity, 6th order
+contributions).
+
+\item{WTURN3=number} (real) (1.0d0) --
+weight of the $U_{turn}^3$ (local-electrostatic cooperativity within 3 residue
+segment, 3rd order contribution).
+
+\item{WTURN4=number} (real) (1.0d0) --
+weight of the $U_{turn}^4$ (local-electrostatic cooperativity within 4 residue
+segment, 4rd order contributions).
+
+\item{WTURN6=number} (real) (1.0d0) --
+weight of the $U_{turn}^6$ (local-electrostatic cooperativity within 6 residue
+segment, 6rd order contributions).
+
+\item{WTOR=number} (real) (1.0d0) --
+weight of the torsional term, $U_{tor}$.
+
+\item{WANG=number} (real) (1.0d0) --
+weight of the virtual-bond angle bending term, $U_b$.
+
+\item{WSCLOC=number} (real) (1.0d0) --
+weight of the side-chain rotamer term, $U_{SC}$.
+
+\item{WSTRAIN=number} (real) (1.0d0) --
+scaling factor of the distance-constrain or disulfide-bond strain energy term.
+
+\item{SCALSCP=number} (real) (1.0d0) --
+scaling factor of $U_{SCp}$; this is an alternative to specifying WSCP; in
+this case WSCP will be calculated as WLONG*SCALSCP.
+
+\item{SCAL14=number} (real) (1.0d0) --
+scaling factor of the 1,4 SC-p interactions.
+
+\item{CUTOFF} (7.0) -- cut-off on backbone-electrostatic interactions to compute 4-
+and higher-order correlations.
+
+\item{DELT\_CORR} (0.5) - thickness of the distance range in which the energy is
+decreased to zero.
+
+\end{description}
+
+The defaults are NOT the recommended values. No ``working'' default values
+have been set, because the force field is still under development. The values
+corresponding to the force fields listed in section 4 are as follows:
+
+CASP3:
+\begin{verbatim}
+WELEC=1.5 WSTRAIN=1.0 WTOR=0.08617 WANG=0.10384 WSCLOC=0.10384 WCORR=1.5 &
+WTURN3=0 WTURN4=0 WTURN6=0 WEL_LOC=0 WCORR5=0 WCORR6=0 SCAL14=0.40 SCALSCP=1.0 &
+CUTOFF=7.00000 WSCCOR=0.0
+\end{verbatim}
+
+ALPHA:
+\begin{verbatim}
+WSC=1.00000 WSCP=0.72364 WELEC=1.10890 WANG=0.68702 WSCLOC=1.79888 &
+WTOR=0.30562 WCORRH=1.09616 WCORR5=0.17452 WCORR6=0.36878 WEL_LOC=0.19508 &
+WTURN3=0.00000 WTURN4=0.55588 WTURN6=0.11539 CUTOFF=7.00000 WCORR4=0.0000 &
+WTORD=0.0 WSCCOR=0.0
+\end{verbatim}
+
+BETA:
+\begin{verbatim}
+WSC=1.00000 WSCP=1.10684 WELEC=0.70000 WANG=0.80775 WSCLOC=1.91939 &
+WTOR=3.36070 WCORRH=2.50000 WCORR5=0.99949 WCORR6=0.46247 WEL_LOC=2.50000 &
+WTURN3=1.80121 WTURN4=4.35377 WTURN6=0.10000 CUTOFF=7.00000 WCORR4=0.00000 &
+WSCCOR=0.0
+\end{verbatim}
+
+ALPHABETA:
+\begin{verbatim}
+WSC=1.00000 WSCP=1.43178 WELEC=0.41501 WANG=0.37790 WSCLOC=0.12880 &
+WTOR=1.98784 WCORRH=2.50526 WCORR5=0.23873 WCORR6=0.76327 WEL_LOC=2.97687 &
+WTURN3=0.09261 WTURN4=0.79171 WTURN6=0.01074 CUTOFF=7.00000 WCORR4=0.00000 &
+WSCCOR=0.0
+\end{verbatim}
+
+CASP5:
+\begin{verbatim}
+WSC=1.00000 WSCP=1.54864 WELEC=0.20016 WANG=1.00572 WSCLOC=0.06764 &
+WTOR=1.70537 WTORD=1.24442 WCORRH=0.91583 WCORR5=0.00607 WCORR6=0.02316 &
+WEL_LOC=1.51083 WTURN3=2.00764 WTURN4=0.05345 WTURN6=0.05282 WSCCOR=0.0 &
+CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
+\end{verbatim}
+
+3P:
+\begin{verbatim}
+WSC=1.00000 WSCP=2.85111 WELEC=0.36281 WANG=3.95152 WSCLOC=0.15244 &
+WTOR=3.00008 WTORD=2.89863 WCORRH=1.91423 WCORR5=0.00000 WCORR6=0.00000 &
+WEL_LOC=1.72128 WTURN3=2.99827 WTURN4=0.59174 WTURN6=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
+\end{verbatim}
+
+4P:
+\begin{verbatim}
+WSC=1.00000 WSCP=2.73684 WELEC=0.06833 WANG=4.15526 WSCLOC=0.16761 &
+WTOR=2.99546 WTORD=2.89720 WCORRH=1.98989 WCORR5=0.00000 WCORR6=0.00000 &
+WEL_LOC=1.60072 WTURN3=2.36351 WTURN4=1.34051 WTURN6=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0
+\end{verbatim}
+
+GAB:
+\begin{verbatim}
+WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &
+WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &
+WVDWPP=0.11371 WHPB=1.00000 &
+CUTOFF=7.00000 WCORR4=0.00000
+\end{verbatim}
+
+E0G:
+\begin{verbatim}
+WLONG=1.70905 WSCP=2.18310 WELEC=1.06684 WBOND=1.00000 WANG=1.17536 &
+WSCLOC=0.22070 WTOR=2.65798 WTORD=2.00646 WCORRH=0.23541 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.42789 WTURN3=1.68126 WTURN4=0.75080 WTURN6=0.00000 &
+WVDWPP=0.27044 WHPB=1.00000 WSCP14=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000
+\end{verbatim}
+
+E0LL2Y:
+\begin{verbatim}
+WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &
+WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &
+WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 &
+CUTOFF=7.00000 WCORR4=0.00000
+\end{verbatim}
+
+\subsubsection{Input and/or reference PDB file name}
+\label{sect:input:main:PDB}
+
+(Text format; subroutine MOLREAD.)
+
+If PDBSTART or PDBREF was specified in the control card, this line contains
+the PDB file name. Trailing slashes to specify the full path are permitted.
+The file name can contain up to 64 characters.
+
+\subsubsection{Amino-acid sequence}
+\label{sect:input:main:sequence}
+
+(Mixed format.)
+
+This data appears, if PDBSTART was not specified, otherwise must not be present
+because the sequence would be taken from the PDB file. The first line contains
+the number of amino-acid residues, including the end groups (free format),
+the next lines contain the sequence in 20(1X,A3) format for the three-letter
+or 80A1 format for the one-letter code. There are two types of end-groups:
+Gly (three-letter code) or G (one-letter code), if an end group contains a full
+peptide bond (e.g., the acetyl N-terminal group or the carboxyamide C-terminal
+group) and D (in the three-letter code) or X (in the one-letter code), if the
+end group does not contain a peptide group (e.g., the NH2 N-terminal end group
+or the COOH C-terminal end group). (Note the Gly or G also denotes the regular
+glycine residue, if found in the middle of a chain).
+In the second case the end group is considered as a ``dummy'' group and serves
+only to define the first (last) virtual-bond dihedral angle $\gamma$ for the
+first (last) full amino-acid residue.
+
+Consider, for example, the Ac-Ala(19)-NHMe polypeptide. The three-letter code
+input will look like this:
+
+\begin{verbatim}
+21
+ Gly Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala
+ Gly
+\end{verbatim}
+
+And the one-letter code input will be:
+
+\begin{verbatim}
+21
+GAAAAAAAAAAAAAAAAAAAG
+\end{verbatim}
+
+If the sequence is changed to NH3(+)-Ala(19)-COO(-), the inputs will look
+like this:
+
+\begin{verbatim}
+21
+ D Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala
+ D
+\end{verbatim}
+
+and
+
+\begin{verbatim}
+21
+XAAAAAAAAAAAAAAAAAAAX
+\end{verbatim}
+
+The sequence input is case-insensitive, because the present version of UNRES
+considers each amino-acid residue as an L-residue (there are no torsional
+parameters for the combinations of the D- and L-residues yet). Furthermore,
+each peptide group is considered as a trans group.
+
+If the version of UNRES has multi-chain capacity, placing a dummy residue
+inside the sequence indicates start of a new chain. For example, a system
+composed of two Ala(10) chains can be specified as follows (3-letter code):
+
+\begin{verbatim}
+23
+ D Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala D Ala Ala Ala Ala Ala Ala Ala Ala
+ Ala Ala D
+\end{verbatim}
+
+or (1-letter code)
+
+\begin{verbatim}
+23
+XAAAAAAAAAAXAAAAAAAAAAX
+\end{verbatim}
+
+\subsubsection{Disulfide-bridge information}
+\label{sect:input:main:disulphide}
+
+(Free format; subroutine READ\_BRIDGE.)
+
+1st line:
+
+NS,(ISS(i),i=1,NS)
+
+\begin{description}
+
+\item{NS} -- the number of half-cystines (required even if no half-cystines are present).
+
+\item{ISS(i)} -- the position of ith half-cystine in the sequence (starting from the
+N-terminal end group)
+
+\end{description}
+
+Next line(s) (present only, if $ns>0$ and must not appear otherwise):
+
+NSS,(IHPB(i),JHPB(i),i=1,NSS)
+
+\begin{description}
+
+\item{NSS} -- the number of disulfide bridges; must not be greater than NS/2.
+
+\item{IHPB(i),JHPB(i)} -- the cystine residue forming the ith bridge.
+
+\end{description}
+
+The program will check, whether the residues specified in the ISS list
+are cystines and terminate with error, if any of them is not. The program
+also checks, if the numbers from the IHPB and the JHPB lists have appeared
+in the ISS list.
+
+\subsubsection{Dihedral-angle restraint data}
+\label{sect:input:main:dihedral-restraints}
+
+(Free format; subroutine MOLREAD.)
+
+This set of data specifies the harmonic constraints (if any) imposed on selected
+virtual-bond dihedral angles $\gamma$.
+
+1st line:
+
+\begin{description}
+
+\item{NDIH\_CONSTR} -- the number of restrained $\gamma$ angles (required even if no
+restrains are applied).
+
+\end{description}
+
+2nd line (present only, if NDIH\_CONSTR$>$0; must not appear otherwise):
+FTORS - the force constant expressed in kcal/(mol*rad**2)
+
+next NDIH\_CONSTR lines (present only, if NDIH\_CONSTR$>$0):
+
+IDIH\_CONSTR(i),PHI0(i),DRANGE(i)
+
+\begin{description}
+
+\item{IDIH\_CONSTR(i)} -- the number of ith restrained $\gamma$ angle. The angles are
+numbered after the LAST $\alpha$-carbons. Thus, the first ``real'' angle has number
+4 and it corresponds to the rotation about the CA(2)-CA(3) virtual-bond axis
+and the last angle has the number NRES and corresponds to the rotation about
+the CA(NRES-2)-CA(NRES-1) virtual-bond axis.
+
+\item{PHI0(i)} -- the ``center'' of the restraint (expressed in degrees).
+
+\item{DRANGE(i)} -- the ``flat well'' range of the restraint (in degrees).
+
+\end{description}
+
+The restraint energy for the ith restrained angle is expressed as:
+
+\begin{displaymath}
+E_{dih} = \begin{cases}
+\rm FTORS\times(\gamma_{IDIH\_CONSTR(i)}-PHI0(i)+DRANGE(i))^2&\mbox{if}\ \ \rm \gamma_{IDIH\_CONSTR(i)}\\
+ &<PHI0(i)+DRANGE(i)\\
+\\
+0 &\rm if\ \ PHI0(i)-DRANGE(i) \\
+ &\le \gamma_{IDIH\_CONSTR(i)} \\
+ &\le PHI0(i)+DRANGE(i)\\
+\\
+\rm FTORS\times(\gamma_{IDIH\_CONSTR(i)}-PHI0(i)+DRANGE(i))^2&\mbox{if}\ \ \rm \gamma_{IDIH\_CONSTR(i)}\\
+ &>PHI0(i)+DRANGE(i)
+\end{cases}
+\end{displaymath}
+
+Applying dihedral-angle constraints also implies that for ith constrained
+$\gamma$ angle the sampling be carried out from the
+[PHI0(i)-DRANGE(i)..PHI0(i)+DRANGE(i)] interval and not from the $[-\pi..\pi]$
+interval, if random conformations are generated. If only this and not
+restrained minimization is required, just set FTORS to 0.
+
+\subsubsection{Distance restraints}
+\label{sect:input:main:disance-restraints}
+
+(Mixed format; subroutine READ\_DIST\_CONSTR.)
+
+Restraints are imposed on C$^\alpha\cdots$C$^\alpha$ SC$\cdots$SC distances (C$^\beta\cdots$C$^\beta$.
+
+\begin{description}
+
+\item{NDIST=number} (integer) (0) -- number of restraints on specific distances.
+
+\item{NFRAG=number} (integer) (0) -- number of distance-restrained protein segments.
+
+\item{NPAIR=number} (integer) (0) -- number of distance-restrained pairs of segments.
+ Specifying NPAIR requires specification of segments.
+
+\item{IFRAG=start(1),end(1),start(2),end(2)...start(NFRAG),end(NFRAG)} (integers) --
+First and last residues of the distance restrained segments.
+
+\item{WFRAG=w(1),w(2),...,w(NFRAG) (reals)} -- force constants or bases for force
+constant calculation corresponding to fragment restraints.
+
+\item{IPAIR=start(1),end(1),start(2),end(2),...,start(NPAIR),end(NPAIR)} (integers)
+-- numbers of segments (consecutive numbers of start or end pairs in IFRAG
+specification), the distances between which will be restrained.
+
+\item{WPAIR=w(1),w(2),...,w(NFRAG)} (reals) -- force constants or bases for force
+constant calculation corresponding to pair restraints.
+
+\item{DIST\_CUT=number} (real) (5.0) -- the cut-off distance in angstroms for force-
+constant calculations.
+
+The force constants within fragments/between pairs of fragments are calculated
+depending on the value of DIST\_CONSTR described in section 5.1:
+
+\begin{description}
+
+\item{1} -- all force constants are equal to the respective entries of WFRAG/WPAIR
+
+\item{2} -- the force constants are equal to the respective entries of WFRAG/WPAIR
+ when the distance between the C$^\alpha$ atoms in the reference structure
+ $\le$D\_CUT, 0 otherwise.
+
+\item{3} -- the force constants are calculated from the formula:
+
+\end{description}
+
+\item{$k(C^\alpha_j,C^\alpha_k)=W\times\exp{-[d(C^\alpha_j,C^\alpha_k)/DIST\_CUT)]^2/2}$}
+
+where $k(C^\alpha_j,C^\alpha_k)$ is the force constant between the respective C$^\alpha$ atoms,
+$d(C^\alpha_j,C^\alpha_k)$ is the distance between these C$^\alpha$ atoms in the reference
+structure, and W is the basis for force-constant calculation (see above).
+
+\end{description}
+
+The above restraints are harmonic resatraints of the form
+
+\begin{displaymath}
+E_{dis} = \sum_i k_i \left(d_i - d_i^{ref}\right)^2
+\end{displaymath}
+
+where $d_i$ is the distance in the calculated structure and $d_i^{ref}$ is the respective
+distance in the reference (PDB) structure. The reference structure is required.
+
+If NDIST$>$0, the restraints on specific distance are input explicitly (no reference structure is requires).
+The restraints are quartic restraints of a similar form as that in section
+\ref{sect:input:main:dihedral-restraints} but with angles replaced with distances.
+
+ihpb(i), jhpb(i), dhpb(i), dhpb1(i), ibecarb(i), forcon(i), i=1,NDIST
+
+\begin{description}
+
+\item{ihpb(i)} and jhpb(i) are the numbers of the residues the distance
+between the C$^\alpha$ atoms of which will be distance restrained,
+
+\item{dhpb(i)} and dhpb1(i) are the lower and upper distance-restraint,
+
+\item{ibecarc(i)} is the restraint-type flag;
+ibecarb(i)==0 indicates that the restraints are imposed on the
+C$^\alpha\cdots$C$^\alpha$ distances; otherwise restraints on the
+SC$\cdots$SC distances are imposed,
+
+\item{forcon(i)}
+is the respective force constant.
+
+\end{description}
+
+\subsubsection{Internal coordinates of the reference structure}
+\label{sect:input:main:internalref}
+
+(Free format; subroutine READ\_ANGLES.)
+
+This part of the data is present, if REFSTR, but not PDBREF was specified,
+otherwise must not appear. It contains the following group of variables:
+
+\begin{description}
+\item{(THETA(i),i=3,NRES)} -- the virtual-bond valence angles THETA.
+\item{(PHI(i),i=4,NRES)} -- the virtual-bond dihedral angles GAMMA.
+\item{(ALPH(i),i=2,NRES-1)} -- the ALPHA polar angles of consecutive side chains.
+\item{(OMEG(i),i=2,NRES-1)} -- the BETA polar angles of consecutive side chains.
+\end{description}
+
+ALPHA(i) and OMEG(i) correspond to the side chain attached to CA(i). THETA(i)
+is the CA(i-2)-CA(i-1)-CA(i) virtual-bond angle and PHI(i) is the
+CA(i-3)-CA(i-2)-CA(i-1)-CA(i) virtual-bond dihedral angle $\gamma$.
+
+\subsubsection{Internal coordinates of the initial conformation}
+\label{sect:input:main:intcoord}
+
+(Free format; subroutine READ\_ANGLES.)
+
+This part of the data is present, if RAND\_CONF, MULTCONF, THREAD, or PDBSTART
+were not specified, otherwise must not appear. This input is as in section \ref{sect:support}.
+
+\paragraph{File name with internal coordinates of the conformations to be processed}
+\label{sect:input:main:intcord:files}
+
+(Text format; subroutine MOLREAD.)
+
+This data is present only, if MULTCONF was specified. It contains the name of
+the file with the internal coordinates. Up to 64 characters are allowed.
+The structure of the file is that of the *.int file produced by UNRES/CSA.
+See section ``The structure of the INT files'' for details.
+
+\subsubsection{Control data for energy map construction}
+\label{sect:input:main:map}
+
+(Data list format; subroutine MAP\_READ.)
+
+These data lists appear, if NMAP=n was specified, where n is the number of
+variables that will be grid-searched. One list is per one variable or a
+group of variables set equal (see below):
+
+\begin{description}
+\item{PHI} -- the variable is a virtual-bond dihedral angle $\gamma$.
+\item{THE} -- the variable is a virtual-bond angle $\theta$.
+\item{ALP} -- the variable is a side-chain polar angle $\alpha$.
+\item{OME} -- the variable is a side-chain polar angle $\beta$.
+\end{description}
+
+\begin{description}
+\item{RES1=number} (integer)
+\item{RES2=number} (integer)
+\end{description}
+
+The range of residues for which the values will be set; all these variables
+will be set at the same value. It is required that RES2$>$RES1.
+
+\begin{description}
+\item{FROM=angle} (real)
+\item{TO=angle} (real)
+\end{description}
+
+Lower and upper limit of scanning in grid search (in degrees)
+
+\begin{description}
+\item{NSTEP=number} (integer)
+\end{description}
+
+Number of steps in scanning along this variable/group of variables.
+
+\subsection{Input coordinate files}
+\label{sect:input:coordfiles}
+
+(Text format; subroutine MOLREAD.)
+
+At present, geometry can be input either from the external files in the PDB
+format (with the PDBSTART option) or multiple conformations can be read
+as virtual-bond-valence and virtual-bond dihedral angles when the MULTCONF
+option is used (the latter, however, implies using standard virtual-bond
+lengths as initial values). The structure of internal-coordinate files
+is the same as that of output internal-coordinate files described in section
+9.1.1.
+
+\subsection{Other input files}
+\label{sect:input:otherfiles}
+
+CSA parameters can optionally be read in free format from file INPUT.CSA.in
+(see section 8.1.4). When a CSA run is restarted, the CSA-specific output files
+also serve as input files. INPUT is the prefix of input and output files
+as explained in section \ref{sect:command}.
+
+Restart files for MD and REMD simulations. They are read when the keyword
+RESTART appears on the MD/REMD data group (section \ref{sect:input:main:MD}).
+
+\newpage
+
+\section{OUTPUT FILES}
+\label{sect:output}
+
+UNRES ``main'' output files (INPUT.out\_\$\{POT\}[processor]) are log files from
+a run. They contain the information of the molecule, force field, calculation
+type, control parameters, etc.; however, not the structures produced during
+the run or their energies except single-point energy evaluation and
+minimization-related runs. The structural information is included in
+coordinate files (*.int, *.x, *.pdb, *.mol2, *.cx) and statistics files (*.stat),
+respectively; these files are further processed by other programs (WHAM,
+CLUSTER) or can be viewed by molecular viewers (pdb or mol2 files).
+
+\subsection{Coordinate files}
+\label{sect:output:coord}
+
+\subsubsection{The internal coordinate (INT) file}
+\label{sect:output:coord:int}
+
+This file contains the internal coordinates of the conformations produced
+by UNRES in non-MD runs. The virtual-bond lengths are assumed constant so
+only the angular variables are provided.
+
+IT,ENER,NSS,(IHPB(I),JHPB(I),I=1,NSS)\\
+(I5,F12.5,I2,9(1X,2I3))
+
+\begin{description}
+\item{IT} -- the number of the conformation.
+\item{ENER} -- total energy.
+\item{NSS} -- the number of disulfide bridges.
+\item{(IHPB(I),JHPB(I),I=1,NSS)} -- the positions of the pairs of half-cystines .
+forming the bridges. If NSS$>9$9, the remaining pairs are written in the
+following lines in the (3X,11(1X,2I3)) format.
+\end{description}
+
+(THETA(I),I=3,NRES)\\
+(8F10.4)
+
+The virtual-bond angles THETA (in degrees)
+
+(PHI(I),I=4,NRES)\\
+(8F10.4)
+
+The virtual-bond dihedral angles GAMMA (in degrees)
+
+(ALPH(I),I=2,NRES-1)\\
+(OMEG(I),I=2,NRES-1)\\
+(8F10.4)
+
+The polar angles ALPHA and BETA of the side-chain centers (in degrees).
+
+\subsubsection{The plain Cartesian coordinate (X) files}
+\label{sect:output:coord:cart}
+
+(Subroutine CARTOUT.)
+
+This file contains the Cartesian coordinates of the $\alpha$-carbon and
+side-chain-center coordinates. All conformations from an MD/MREMD
+trajectory are collated to a single file. The structure of each
+conformation's record is as follows:
+
+1st line: time, potE, uconst, t\_bath,nss, (ihpb(j), jhpb(j), j=1,nss),
+nrestr, (qfrag(i), i=1,nfrag), (qpair(i), i=1,npair),
+(utheta(i), ugamma(i), uscdiff(i), i=1,nfrag\_back)
+
+\begin{description}
+\item{time:} MD time (in ``molecular time units'' 1 mtu = 4.89 fs),
+\item{potE:} potential energy,
+\item{uconst:} restraint energy corresponding to restraints on Q and backbone geometry,
+(see section \ref{sect:input:main:MD}),
+\item{t\_bath:} thermostat temperature,
+\item{nss:} number of disulfide bonds,
+\item{ihpb(j), jhpb(j):} the numbers of linked cystines for jth disulfide bond,
+\item{nrestr:} number of restraints on q and local geometry,
+\item{qfrag(i):} q value for ith fragment,
+\item{qpair(i):} q value for ith pair,
+\item{utheta(i):} sum of squares of the differences between the theta angles
+ of the current conformation from those of the experimental conformation,
+\item{ugamma(i):} sum of squares of the differences beaten the gamma angles
+ of the current conformation from those of the experimental conformation,
+\item{uscdiff(i):} sum of squares of the differences between the Cartesian difference
+ of the unit vector of the C$^\alpha$-SC axis of the current conformation from
+ those of the experimental conformation.
+\end{description}
+
+Next lines: Cartesian coordinates of the C$^\alpha$ atoms (including dummy atoms)
+(sequentially, 10 coordinates per line)
+Next lines: Cartesian coordinates of the SC atoms (including glycines and
+dummy atoms) (sequentially, 10 coordinates per line)
+
+\subsubsection{The compressed Cartesian coordinate (CX) files}
+\label{sect:output:coord:cx}
+
+These files are compressed binary files (extension cx). For each conformation,
+the items are written in the same order as specified in section \ref{sect:output:coord:cx}. For
+MREMD runs, if TRAJ1FILE is specified on MREMD record (see section \ref{sect:input:main:MD}),
+snapshots from all trajectories are written every time the coordinates
+are dumped. Thus, the file contains snapshot 1 from trajectory 1, ...,
+snapshot 1 from trajectory M, snapshot 2 from trajectory 1, ..., etc.
+
+The compressed cx files can be converted to pdb file by using the xdrf2pdb
+auxiliary program (single trajectory files) or xdrf2pdb-m program (multiple
+trajectory files from MREMD runs generated by using the TRAJ1FILE option).
+The multiple-trajectory cx files are also input files for the auxiliary
+WHAM program.
+
+\subsubsection{The Brookhaven Protein Data Bank format (PDB) files}
+\label{sect:output:coord:PDB}
+
+(Subroutine PDBOUT.)
+
+\sloppy
+These files are written in PDB standard (see. e.g.,
+\href{ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf}{\textcolor{blue}{ftp://ftp.wwpdb.org/pub/pdb\-/doc/\-format\_descriptions}}). %\-/Format\_v33\_Letter.pdf}.
+The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used.
+The C$^\alpha$ (marked CA) and SC (marked CB) coordinates are output. The CONECT
+records specify the C$^\alpha\cdots$C$^\alpha$ and C$^\alpha\cdots$SC virtual bonds. Secondary
+structure is detected based on peptide-group contacts, as specified in
+ref 12. Dummy residues are omitted from the output. If the program has
+multiple-chain function, the presence of a dummy residue in a sequence
+starts a new chain, which is assigned the next alphabet letter as ID, and
+residue numbering is started over.
+
+\subsubsection{The SYBYLL (MOL2) files}
+\label{sect:output:coord:subyll}
+
+See the description of mol2 format (e.g.,
+\href{http://tripos.com/data/support/mol2.pdf}{http://tripos.com/data/support/mol2.pdf}.
+Similar remarks apply as for
+the PDB format (section \ref{sect:output:coord:PDB}).
+
+\subsection{The summary (STAT) file}
+
+\subsubsection{Non-MD runs}
+
+This file contains a short summary of the quantities characterizing the
+conformations produced by UNRES/CSA. It is created for MULTCONF and MCM.
+
+NOUT,EVDW,EVDW2,EVDW1+EES,ECORR,EBE,ESCLOC,ETORS,ETOT,RMS,FRAC\\
+(I5,9(1PE14.5))
+
+\begin{description}
+\item{NOUT} -- the number of the conformations
+\item{EVDW,EVDW2,EVDW1+EES,ECORR,EBE,ESCLOC,ETORS} -- energy components
+\item{ETOT} -- total energy
+\item{RMS} -- RMS deviation from the reference structure (if REFSTR was specified)
+\item{FRAC} -- fraction of side chain - side chain contacts of the reference
+ structure present in this conformation (if REFSTR was specified)
+\end{description}
+
+\subsubsection{MD and MREMD runs}
+\label{sect:output:coord:MD}
+
+Each line of the stat file generated by MD/MREMD runs contains the following
+items in sequence:
+
+\begin{description}
+\item{step} -- the number of the MD step
+\item{time} -- time [unit is MTU (molecular time unit) equal to 48.9 fs]
+\item{Ekin} -- kinetic energy [kcal/mol]
+\item{Epot} -- potential energy [kcal/mol]
+\item{Etot} -- total energy (Ekin+Epot)
+\item{H-H0} -- the difference between the cureent and initial extended Hamiltionian
+ in Nose-Hoover or Nose-Poincare runs; not present for other thermostats.
+\item{RMSD} -- root mean square deviation from the reference structure (only in
+ REFSTR has been specified)
+item{damax} -- maximum change of acceleration between two MD steps
+\item{fracn} -- fraction of native side-chain concacts (very crude, based on
+ SC-SC distance only)
+\item{fracnn} -- fraction of non-native side-chain contacts
+\item{co} -- contact order
+\item{temp} -- actual temperature [K]
+\item{T0} -- initial (microcanonical runs) or thermostat (other run types)
+ temperature [K]
+\item{Rgyr} -- radius of gyration based on C$^\alpha$ coordinates [A]
+\item{proc} -- in MREMD runs the number of the processor (the number of the
+ trajectory less 1); not present for other runs.
+\end{description}
+
+For an USAMPL run, the following items follow the above list:
+
+\begin{description}
+\item{iset} -- the number of the restraint set
+\item{uconst} -- restraint energy pertaining to q-values
+\item{uconst\_back} -- restraint energy pertaining to virtual-backbone restraints
+\item{(qfrag(i),i=1,nfrag)} -- q values of the specified fragments
+\item{(qpair(ii2),ii2=1,npair)} -- q values of the specified pairs of fragments
+\item{(utheta(i),ugamma(i),uscdiff(i),i=1,nfrag\_back)} -- virtual-backbone and
+ side-chain-rotamer restraint energies of the fragments specified
+\end{description}
+
+If PRINT\_COMPON has been specified, the energy components are printed
+after the items described above.
+
+\subsection{CSA-specific output files}
+\label{sect:output:coord:CSA}
+
+There are several output files from the CSA routine:
+INPUT.CSA.seed, INPUT.CSA.history, INPUT.CSA.bank, INPUT.CSA.bank1,
+INPUT.CSA.rbank INPUT.CSA.alpha, INPUT.CSA.alpha1.
+
+The most informative outfile is INPUT.CSA.history. This file first write down
+the parameters in INPUT.CSA.csa file. Later it shows the energies of random
+minimized conformations in its generation. After sorting the First\_bank
+in energy (ascending order), the energies of the First\_bank is re-written here.
+After this the output looks like:
+
+\begin{verbatim}
+ 1 0 100 6048.2 1 100-224.124-114.346 202607 100 100
+ 1 0 700 5882.6 2 29-235.019-203.556 1130308 100 100
+ 1 0 1300 5721.5 2 18-242.245-212.138 2028008 100 100
+ 1 0 1900 5564.8 13 54-245.185-218.087 2897988 98 100
+ 1 0 2500 5412.4 13 61-246.214-222.068 3706478 97 100
+ 1 0 3100 5264.2 13 89-248.715-224.939 4514196 96 100
+\end{verbatim}
+
+Each line is written between each iteration (just after selection
+of seed conformations) containing following data:
+jlee,icycle,nstep,cutdif,ibmin,ibmax,ebmin,ebmax,nft,iuse,nbank
+ibmin and ibmax lists the index of bank conformations corresponding to the
+lowest and highest energies with ebmin and ebmax.
+nft is the total number of function evaluations so far.
+iuse is the total number of conformations which have not been used as seeds
+prior to calling subroutine select\_is which select seeds.
+
+Therefore, in the example shown above, one notes that so far 3100
+minimizations has been performed corresponding to the total of 4514196
+function evaluations. The lowest and highest energy in the Bank is
+-248.715 (\#13) and -224.939 (\#89), respectively. The number of conformations
+already used as seeds (not including those selected as seeds in this iteration)
+so far is 4 (100-96).
+
+The files INPUT.CSA.bank and INPUT.CSA.rbank contains data of Bank and
+First\_bank. For more information on these look subroutines write\_bank
+and write\_rbank. The file INPUT.CSA.bank is overwritten between each
+iteration whereas Bank is accumulated in INPUT.CSA.bank1 (not for every
+iteration but as specified in the subroutine together.f).
+
+The file INPUT.CSA.seed lists the index of the seed conformations with their
+energies. Files INPUT.CSA.alpha, INPUT.CSA.alpha1 are written only once
+at the beginning of the CSA run. These files contain some arrays used
+in CSA procedure.
+
+\newpage
+
+\section{TECHNICAL SUPPORT CONTACT INFORMATION}
+\label{sect:support}
+
+ Dr. Adam Liwo\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ phone: +48 58 523 5124\\
+ fax: +48 58 523 5012\\
+ e-mail: \href{mailto:adam@sun1.chem.univ.gda.pl}{adam@sun1.chem.univ.gda.pl}\\
+
+ Dr. Cezary Czaplewski\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ phone: +48 58 523 5126\\
+ fax: +48 58 523 5012\\
+ e-mail: \href{mailto:cezary.czaplewski@ug.edu.pl}{cezary.czaplewski@ug.edu.pl}\\
+
+ Dr. Adam Sieradzan\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ phone: +48 58 523 5124\\
+ fax: +48 58 523 5012\\
+ e-mail: \href{mailto:adasko@sun1.chem.univ.gda.pl}{adasko@sun1.chem.univ.gda.pl}\\
+
+ Dr. Stanislaw Oldziej\\
+ Intercollegiate Faculty of Biotechnology\\
+ University of Gdansk, Medical University of Gdansk\\
+ ul. Kladki 22, 80-922 Gdansk, Poland\\
+ phone: +48 58 523 5361\\
+ fax: +48 58 523 5472\\
+ e-mail: \href{mailto:stan@biotech.ug.edu.pl}{stan@biotech.ug.edu.pl}\\
+
+ Dr. Jooyoung Lee\\
+ Korea Institute for Advanced Study\\
+ 207-43 Cheongnyangni 2-dong, Dongdaemun-gu,\\
+ Seoul 130-722, Korea\\
+ phone: +82-2-958-3890\\
+ fax: +82-2-958-3731\\
+ email: \href={mailto:jlee@kias.re.kr}{jlee@kias.re.kr}
+
+\small{
+ Prepared by Adam Liwo and Jooyoung Lee, 7/17/99\\
+ Revised by Cezary Czaplewski 1/4/01\\
+ Revised by Cezary Czaplewski and Adam Liwo 8/26/03\\
+ Revised by Cezary Czaplewski and Adam Liwo 11/26/11\\
+ Revised by Adam Liwo 02/19/12\\
+ LaTeX version by Adam Liwo 09/25/12\\
+ revised by Adam Liwo 12/04/14
+}
+\end{document}
--- /dev/null
+\documentclass[12pt]{article}
+%\usepackage{latex2html}
+\usepackage{enumerate}
+\usepackage{longtable}
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{color}
+\parindent=0pt
+\parskip=12pt
+\textheight=24cm
+\textwidth=18cm
+\topmargin=-2.5cm
+\oddsidemargin=-0.5cm
+\setcounter{secnumdepth}{5}
+\setcounter{tocdepth}{5}
+\begin{document}
+\sloppy
+
+\title{WHAM \\ (Weighted Histogram Analysis Method)\\
+ Processing results of UNRES/MREMD simulations}
+
+\author{Laboratory of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Wita Stwosza 63\\ 80-308 Gdansk, Poland\\
+\\
+\\
+Scheraga Group\\ Baker Laboratory of Chemistry \\
+and Chemical Biology\\ Cornell University\\ Ithaca, NY 14853-1301, USA}
+
+\maketitle
+
+\newpage
+
+\tableofcontents
+
+%1. License terms
+%2. References
+%3. Functions of the program
+%4. Installation
+%5. Running the program
+%6. Input and output files
+%6.1. Summary of files
+%6.2. The main input file
+%6.2.1. General data
+%6.2.2. Molecule and energy parameter data
+%6.2.2.1. General information
+%6.2.2.2. Sequence information
+%6.2.2.3. Dihedral angle restraint information
+%6.2.2.4. Disulfide-bridge data
+%6.2.3. Energy-term weights and parameter files
+%6.2.4. (M)REMD/Hamiltonian (M)REMD setting specification
+%6.2.5. Information of files from which to read conformations
+%6.2.6. Information of reference structure and comparing scheme
+%6.3. The structure of the main output file (out)
+%6.4. The thermodynamic quantity and ensemble average (stat) files
+%6.5. The conformation summary with classification (stat) files
+%6.6. The histogram files
+%6.7. The rmsd-radius of gyration potential of mean force files
+%6.8. The PDB files
+%6.9. The compresses Cartesian coordinates (cx) file
+%7. Support
+
+\newpage
+
+\section{LICENSE TERMS}
+\label{sect:license}
+
+\begin{itemize}
+
+\item
+ This software is provided free of charge to academic users, subject to the condition that no part of it be sold or used otherwise for commercial purposes, including, but not limited to its incorporation into commercial software packages, without written consent from the authors. For permission contact Prof. H. A. Scheraga, Cornell University.
+
+\item
+ This software package is provided on an ``as is'' basis. We in no way warrant either this software or results it may produce.
+
+\item
+ Reports or publications using this software package must contain an acknowledgment to the authors and the NIH Resource in the form commonly used in academic research.
+
+\end{itemize}
+
+\newpage
+
+\section{REFERENCES}
+\label{sect:references}
+
+Citing the following references in your work that makes use of the WHAM software is gratefully
+acknowledged:
+
+\begingroup
+\renewcommand{\section}[2]{}%
+\begin{thebibliography}{10}
+
+\bibitem{kumar_1992}
+S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, J.M. Rosenberg.
+The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method.
+{\it J. Comput. Chem.}, {\bf 1992}, 13, 1011-1021.
+
+\bibitem{liwo_2007}
+A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, K. Wachucik, H.A. Scheraga.
+Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.
+{\it J. Phys. Chem. B}, {\bf 2007}, 111, 260-285.
+
+\bibitem{oldziej_2004}
+S. Oldziej, A. Liwo, C. Czaplewski, J. Pillardy, H.A. Scheraga.
+Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 2. Off-lattice tests of the method with single proteins.
+{\it J. Phys. Chem. B}, {\bf 2004}, 108, 16934-16949.
+
+\end{thebibliography}
+
+\endgroup
+
+\newpage
+
+\section{FUNCTIONS OF THE PROGRAM}
+\label{sect:func}
+
+The program processes the results of replica exchange (REMD) or multiplexed replica exchange molecular
+dynamics (MREMD) simulations with UNRES to compute the probabilities of the obtained conformations to
+occur at particular temperatures. The program is based on the variant of the weighted histogram analysis
+(WHAM) method \cite{kumar_1992} described in ref \cite{liwo_2007}.
+
+The program outputs the following information:
+
+\begin{enumerate}[(a)]
+
+\item
+Temperature profiles of thermodynamic and structural ensemble-averaged quantities.
+
+\item
+Histograms of native-likeness measure q (defined by eqs 8-11 of ref [\cite{liwo_2007}]).
+
+\item
+Optionally the most probable conformations at REMD temperatures.
+
+\item
+Optionally the coordinates with information to compute probabilities for the conformations to occur at any temperature.
+
+\end{enumerate}
+
+The program takes usually UNRES compressed coordinate files (cx files) from MREMD obtained by using the TRAJ1FILE option. The user can request to partition the whole run into equal slices (or windows), each starting from, say, snapshot n (for each trajectory) and ending at snapshot n+1.
+Alternatively, the UNRES Cartesian coordinate (x files) can be input; however, they must contain only the analyzed portion of the trajectories; they are usually prepared from single trajectories by using xdrf2x.
+
+Two versions of the program are provided:
+
+\begin{enumerate}[(a)]
+
+\item
+Canonical version which treats single polypeptide chains; the source code is in WHAM/src directory.
+
+\item
+Version for oligomeric proteins; multiple chains are handled by inserting dummy residues in the sequence; the source code is in WHAM/src-M directory.
+
+\end{enumerate}
+
+\newpage
+
+\section{INSTALLATION}
+\label{sect:install}
+
+It is recommended to use Cmake to install the entire package; see the Installation Guide for instructions.
+Step-by-step installation without Cmake is also possible; please follow section 4 of Installation Guide for general
+information.
+
+Customize Makefile to your system. See section 7 of the description of UNRES for compiler flags that are used to created executables for a particular force field. There are already several Makefiles prepared for various systems and force fields.
+
+Run make in the WHAM/src directory WHAM/src-M directory for multichain version. Make sure that MPI is installed on your system; the present program runs only in parallel mode.
+
+\newpage
+
+\section{RUNNING THE PROGRAM}
+\label{sect:running}
+
+The program requires a parallel system to run. Depending on system, either the wham.csh C-shell script (in WHAM/bin directory) can be started using mpirun or the binary in the C-shell script must be executed through mpirun. See the wham.csh C-shell script and section 6 for the files processed by the program.
+
+\newpage
+
+\section{INPUT AND OUTPUT FILES}
+\label{sect:inoutfiles}
+
+\subsection{Summary of the files}
+\label{sect:inoutfiles:summary}
+The C-shell script wham.csh is used to run the program (see the WHAM/bin directory). The data files that the script needs are mostly the same as for UNRES (see section 6 of UNRES description). In addition, the environmental variable CONTFUN specifies the method to assess whether two side chains are at contact; if CONTFUN=GB, the criterion defined by eq 8 of ref 4 is used to assess whether two side chains are at contact. Also, the parameter files from the C-shell scripts are overridden if the data from Hamiltonian MREMD are processed; if so, the parameter files are defined in the main input file.
+
+The main input file must have inp extension. If it is INPUT.inp, the output files are as follows:
+
+\begin{description}
+
+\item{INPUT.out\_POTxxx} -- output files from different processors (INPUT.out\_000 is the main output file). POT is the identifier of the sidechain-sidechain potential.
+
+\item{INPUT\_POT\_GB\_xxx.stat} or INPUT\_POT\_slice\_YYXXX.stat -- the summary conformation-classification file from processor xxx (each processor handles part of conformations); the second occurs if the run is partitioned into slices.
+
+\item{INPUT.thermal} or INPUT\_slice\_yy.thermal -- thermodynamic functions and temperature profiles of the ensemble averages (the second form if the run is partitioned into slices).
+
+\item{INPUT\_T\_xxx.pdb} or INPUT\_slice\_yy\_T\_xxx.pdb -- top conformations the number of these conformations is selected by the user) in PDB format.
+
+\item{INPUT.cx} -- the compressed UNRES coordinate file with information to compute the probability of a given conformation at any temperature.
+
+\item{INPUT.hist}, INPUT\_slice\_xx.hist, INPUT\_par\_yy.hist, INPUT\_par\_yy\_slice\_zz.x -- histograms of q at MREMD temperatures.
+
+\item{INPUT.ent}, INPUT\_slice\_xx.ent, INPUT\_par\_yy.ent, INPUT\_par\_yy\_slice\_xx.ent -- the histogram(s) of energy density.
+
+\item{INPUT.rmsrgy}, INPUT\_par\_yy.rmsrgy, INPUT\_slice\_xx.rmsrgy or INPUT\_par\_yy\_slice\_xx.rmsrgy -- the 2D histogram(s) of rmsd from the experimental structure and radius of gyration.
+
+\end{description}
+
+\subsection{Main input file}
+\label{sect:inoutfiles:main}
+
+This file has the same structure as the UNRES input file; most of the data are input in a keyword-based form (see section 7.1 of UNRES description). The data are grouped into records, referred to as lines. Each record, except for the records that are input in non-keyword based form, can be continued by placing an ampersand (\&) in column 80. Such a format is referred to as the data list format.
+
+In the following description, the default values are given in parentheses.
+
+\subsubsection{General data (data list format)}
+\label{sect:inoutfiles:main:general}
+
+\begin{description}
+
+\item{N\_ENE} (N\_ENE\_MAX) -- the number of energy components.
+
+\item{SYM} (1) -- number of chains with same sequence (for oligomeric proteins only).
+
+\item{HAMIL\_REP} -- if present, Hamiltonian process the results of replica exchange runs (replicas with different parameters of the energy function).
+
+\item{NPARMSET} (1) -- number of energy parameter sets ($>$1 only for Hamiltonian replica exchange simulations).
+
+\item{SEPARATE\_PARSET} -- if present, HREMD was run in a mode such that only temperature but not energy-function parameters was exchanged.
+
+\item{IPARMPRINT} (1) -- number of parameter set with which to construct conformational ensembles; important only when HREMD runs are processed.
+
+\item{ENE\_ONLY} -- if present, only conformational energies will be calculated and printed; no WHAM iteration.
+
+\item{EINICHECK} (2) -- $>0$ compare the conformational energies against those stored in the coordinate file(s); 1: compare but print only a warning message if different; 2: compare and terminate the program if different; 0: don't compare.
+
+\item{MAXIT} (5000) -- maximum number of iterations in solving WHAM equations.
+
+\item{ISAMPL} (1) -- input conformation sampling frequency (e.g., if ISAMPL=5, only each 5th conformation will be read).
+
+\item{NSLICE} (1) -- number of ``slices'' or ``windows'' into which each trajectory will be partitioned; each slice will be analyzed independently.
+
+\item{FIMIN} (0.001) -- maximum average difference between window free energies between the current and the previous iteration.
+
+\item{ENSEMBLES} (0) -- number of conformations (ranked according to probabilities) to be output to PDB file at each MREMD temperature; 0 means that no conformations will be output. Non-zero values should not be used when NSLICE$>$1.
+
+\item{CLASSIFY} -- if present, each conformation will be assigned a class, according to the scheme described in
+ref \cite{oldziej_2004}.
+
+\item{DELTA} (0.01) -- one dimension bin size of the histogram in q.
+
+\item{DELTRMS} (0.05) -- rms dimension bin size in rms-radius of gyration histograms.
+
+\item{DELTRGY} (0.05) - radius of gyration bin size in rms-radius of gyration histograms.
+
+\item{NQ} (1) -- number of q's (can be for entire molecule, fragments, and pairs of fragments).
+
+\item{CXFILE} -- produce the compressed coordinate file with information necessary to compute the probabilities of conformations at any temperature.
+
+\item{HISTOUT} -- if present, the histograms of q at MREMD temperatures are constructed and printed to main output file.
+
+\item{HISTFILE} -- if present, the histograms are also printed to separate files.
+
+\item{ENTFILE} -- if present, histogram of density of states (entropy) is constructed and printed.
+
+\item{RMSRGYMAP} -- if present, 2D histograms of radius of rmsd and radius of gyration at MREMD temperatures are constructed and printed.
+
+\item{WITH\_DIHED\_CONSTR} -- if present, dihedral-angle restraints were imposed in the processed MREMD simulations.
+
+\item{RESCALE} (1) -- Choice of the type of temperature dependence of the force field.
+
+\begin{description}
+
+\item{$>0$} -- no temperature dependence.
+
+\item{1} -- homographic dependence (not implemented yet with any force field).
+
+\item{2} -- hyperbolic tangent dependence \cite{liwo_2007}.
+
+\end{description}
+
+\end{description}
+
+\subsubsection{Molecule data}
+\label{sect:inoutfiles:main:molecule}
+
+\paragraph{General information}
+\label{sect:inoutfiles:main:molecule:geninfo}
+
+\begin{description}
+
+\item{SCAL14} (0.4) -- scale factor of backbone-electrostatic 1,4-interactions.
+
+\item{SCALSCP} (1.0) -- scale factor of SC-p interactions.
+
+\item{CUTOFF} (7.0) -- cut-off on backbone-electrostatic interactions to compute 4- and higher-order correlations.
+
+\item{DELT\_CORR} (0.5) -- thickness of the distance range in which the energy is decreased to zero.
+
+\item{ONE\_LETTER} -- if present, the sequence is to be read in 1-letter code, otherwise 3-letter code.
+
+\end{description}
+
+\paragraph{Sequence information \\ \\}
+\label{sect:inoutfiles:main:molecule:sequence}
+
+
+1st record (keyword-based input):
+
+NRES -- number of residues, including the UNRES dummy terminal residues, if present
+
+Next records: amino-acid sequence
+
+3-letter code: Sequence is input in format 20(1X,A3)
+
+1-letter code: Sequence is input in format 80A1
+
+\paragraph{Dihedral angle restraint information \\ \\}
+\label{sect:inoutfiles:main:molecule:restraints}
+
+
+This is the information about dihedral-angle restraints, if any are present.
+It is specified only when WITH\_DIHED\_CONSTR is present in the first record.
+
+1st line: ndih\_constr -- number of restraints (free format).
+
+2nd line: ftors -- force constant (free format).
+
+Each of the following ndih\_constr lines:
+
+idih\_constr(i),phi0(i),drange(i) (free format)
+
+\begin{description}
+
+\item{idih\_constr(i)} -- the number of the dihedral angle gamma corresponding to the ith restraint.
+
+\item{phi0(i)} -- center of dihedral-angle restraint.
+
+\item{drange(i)} -- range of flat well (no restraints for phi0(i) +/- drange(i)).
+
+\end{description}
+
+\paragraph{Disulfide-bridge data\\ \\}
+\label{sect:inoutfiles:main:molecule:disulfide}
+
+
+1st line: NS, (ISS(I),I=1,NS) (free format)
+
+\begin{description}
+
+\item{NS} -- number of cystine residues forming disulfide bridges.
+
+\item{ISS(I)} -- the number of the Ith disulfide-bonding cystine in the sequence.
+
+\end{description}
+
+nd line: NSS, (IHPB(I),JHPB(I),I=1,NSS) (free format)
+
+\begin{description}
+
+\item{NSS} -- number of disulfide bridges
+
+\item{IHPB(I),JHPB(I)} - the first and the second residue of ith disulfide link
+
+\end{description}
+
+Because the input is in free format, each line can be split.
+
+\subsubsection{Energy-term weights and parameter files}
+\label{sect:inoutfiles:main:weights}
+
+There are NPARMSET records specified below.
+All items described in this section are input in keyword-based mode.
+
+1st record: Weights for the following energy terms:
+
+\begin{description}
+
+\item{WSC} (1.0) -- side-chain-side-chain interaction energy.
+\item{WSCP} (1.0) -- side chain-peptide group interaction energy.
+\item{WELEC} (1.0) -- peptide-group-peptide group interaction energy.
+\item{WEL\_LOC (1.0)} -- third-order backbone-local correlation energy.
+\item{WCORR} (1.0) -- fourth-order backbone-local correlation energy.
+\item{WCORR5} (1.0) -- fifth-order backbone-local correlation energy.
+\item{WCORR6} (1.0) -- sixth-order backbone-local correlation energy.
+\item{WTURN3} (1.0) -- third-order backbone-local correlation energy of pairs of peptide groups separated by a single peptide group.
+\item{WTURN4} (1.0) -- fourth-order backbone-local correlation energy of pairs of peptide groups separated by two peptide groups.
+\item{WTURN6} (1.0) -- sixth-order backbone-local correlation energy for pairs of peptide groups separated by four peptide groups.
+\item{WBOND} (1.0) -- virtual-bond-stretching energy.
+\item{WANG} (1.0) -- virtual-bond-angle-bending energy.
+\item{WTOR} (1.0) -- virtual-bond-torsional energy.
+\item{WTORD} (1.0) -- virtual-bond-double-torsional energy.
+\item{WSCCOR} (1.0) -- sequence-specific virtual-bond-torsional energy.
+\item{WDIHC} (0.0) -- dihedral-angle-restraint energy.
+\item{WHPB} (1.0) -- distance-restraint energy.
+
+\end{description}
+
+2nd record: Parameter files. If filename is not specified that corresponds to particular parameters, the respective name from the C-shell script will be assigned. If no files are to be specified, an empty line must be inserted.
+
+\begin{description}
+\item{BONDPAR} -- bond-stretching parameters.
+\item{THETPAR} -- backbone virtual-bond-angle-bending parameters.
+\item{ROTPAR} -- side-chain-rotamer parameters.
+\item{TORPAR} -- backbone-torsional parameters.
+\item{TORDPAR} -- backbone-double-torsional parameters.
+\item{FOURIER} -- backbone-local -- backbone-electrostatic correlation parameters.
+\item{SCCORAR} -- sequence-specific backbone-torsional parameters (not used at present).
+\item{SIDEPAR} -- side-chain-side-chain-interaction parameters.
+\item{ELEPAR} -- backbone-electrostatic-interaction parameters.
+\item{SCPPAR} -- backbone-side-chain-interaction parameters.
+\end{description}
+
+\subsubsection{(M)REMD/Hamiltonian (M)REMD setting specification}
+\label{sect:inoutfiles:main:MREMD}
+
+If HAMIL\_REP is present in general data, read the following group of records only once; otherwise, read for each parameter set (NPARSET times total).
+
+\begin{description}
+
+\item{NT} (1) -- number of temperatures.
+
+\item{REPLICA} -- if present, replicas in temperatures were specified with this parameter set.
+
+\item{UMBRELLA} -- if present, umbrella-sampling was run with this parameter set.
+
+\item{READ\_ISET} -- if present, umbrella-sampling-window number is read from the compressed Cartesian coordinate (cx) file even if the data are not from umbrella-sampling run(s). ISET is present in the cx files from the present version of UNRES.
+
+\end{description}
+
+Following NT records are for consecutive temperature replicas; each record is
+organized as keyword-based input:
+
+\begin{description}
+
+\item{TEMP} (298.0) - initial temperature of this replica (replicas in MREMD).
+
+\item{FI} (0.0) - initial values of the dimensionless free energies for all q-restraint windows for this replica (NR values).
+
+\item{KH} (100.0) - force constants of q restraints (NR values).
+Q0 (0.0d0) - q-restraint centers (NR values)</p>
+
+\end{description}
+
+\subsubsection{Information of files from which to read conformations}
+\label{sect:inoutfile:main:conffiles}
+
+If HAMIL\_REP is present in general data, read the following two records only once; otherwise, read for each parameter set (NPARSET times total).
+
+1st record (keyword-based input):.
+
+For temperature replica only ONE record is read; for non-(M)REMD runs, NT records must be supplied. The records are in keyword-based format.
+
+\begin{description}
+\item{NFILE\_ASC} -- number of files in ASCII format (UNRES Cartesian coordinate (x) files) for current parameter set.
+
+\item{NFILE\_CX} -- number of compressed coordinate files (cx files) for current parameter set.
+
+\item{NFILE\_BINi} -- number of binary coordinate files (now obsolete because it requires initial conversion of ASCII format trajectories into binary format).
+
+\end{description}
+
+It is strongly recommended to use cx files from (M)REMD runs with TRAJ1FILE option. Multitude of trajectory files which are opened and closed by different processors might impair file system accessibility. Should you wish to process trajectories each one of which is stored in a separate file, better collate the required slices of them first to an x file by using the xdrf2x program piped to the UNIX cat command.
+
+coordinate file name(s) without extension.
+
+\subsubsection{Information of reference structure and comparing scheme}
+\label{sect:inoutfile:main:reference}
+
+The following records pertain to setting up the classification of conformation aimed ultimately at obtaining a class numbers. Fragments and pairs of fragments are specified and compared against those of reference structure in terms of secondary structure, number of contacts, rmsd, virtual-bond-valence and dihedral angles, etc. Then the class number is constructed as described in ref 3. A brief description of comparison procedure is as follows:
+
+\begin{enumerate}
+
+\item
+Elementary fragments usually corresponding to elements of secondary or supersecondary structure are selected. Based on division into fragments, levels of structural hierarchy are defined.
+
+\item
+At level 1, each fragment is checked for agreement with the corresponding fragment in the native structure. Comparison is carried out at two levels: the secondary structure agreement and the contact-pattern agreement level.
+
+At the secondary structure level the secondary structure (helix, strand or undefined) in the fragment is compared with that in the native fragment in a residue-wise manner. Score 0 is assigned if the structure is different in more than 1/3 of the fragment, 1 is assigned otherwise.
+
+The contact-pattern agreement level compares the contacts between the peptide groups of the backbone of the fragment and the native fragment and also compares their virtual-bond dihedral angles gamma. It is allowed to shift the sequence by up to 3 residues to obtain contact pattern match. A score of 0 is assigned if more than 1/3 of native contacts do not occur or there is more than 60 deg (usually, but this cutoff can be changed) maximum difference in gamma. Otherwise score 1 is assigned.
+
+The total score of a fragment is an octal number consisting of bits hereafter referred to S (secondary structure) C (contact match) and H (sHift) (they are in the order HCS). Their values are as follows:
+
+\begin{description}
+\item{S} -- 1 native secondary structure; 0 otherwise,
+\item{C} -- 1 native contact pattern; 0 otherwise,
+\item{H} -- 1 contact match obtained without sequence shift 0 otherwise.
+\end{description}
+
+For example,
+octal 7 (111) corresponds to native secondary structure, native contact pattern, and no need to shift the sequence for contact match;
+octal 1 (001) corresponds to native secondary structure only (i.e., nonnative contact pattern).
+
+\item
+At level 2, contacts between (i) the peptide groups or (ii) the side chains within pairs of fragments are compared. Case (i) holds when we seek contacts between the strands of a larger beta-sheet formed by two fragments, case (ii) when we seek the interhelix or helix-beta sheet contacts. Additionally, the pairs of fragments are compared with their native counterparts by rmsd.
+
+Score 0 is assigned to a pair of fragments, if it has less than 2/3 native contacts and too large rmsd (a cut-off of 0.1 A/residue is set), score 1 if it has enough native contacts and sufficiently low rmsd, but the sequence has to be shifted to obtain a match, and score 2, if sufficient match is obtained without shift.
+
+\item
+At level 3 and higher, triads, quadruplets,..., etc. of fragments are compared in terms of rmsd from their native counterparts (the last level corresponds to comparing whole molecules). The score (0, 1, or 2) is assigned to each composite fragment as in the case of level 2.
+
+\item
+The TOTAL class number of a structure is a binary number composed of parts of scores of fragments, fragment pairs, etc. It is illustrated on the following example; it is assumed that the molecule has three fragment as in the case of 1igd.
+
+\end{enumerate}
+
+\begin{verbatim}
+level 1 level 2 level 3
+123 123 123||1-2 1-3 2-3 1-2 1-3 2-3 || 1-2-3 | 1-2-3 ||
+sss|ccc|hhh|| c c c | h h h || r | h ||
+\end{verbatim}
+
+Bits s, c, and h of level 1 are explained in point 2; bits c and h of level 2 pertain to contact-pattern match and shift; bits r and h of level 3 pertain to rmsd match and shift for level 3.
+
+The input is specified as follows:
+
+1st record (keyword-based input):
+
+\begin{description}
+
+\item{VERBOSE} -- if present, detailed output in classification (use if you want to fill up the disk).
+
+\item{PDBREF} -- if present, the reference structure is read from the pdb.
+
+\item{BINARY} -- if present, the class will be output in octal/quaternary/binary format for levels 1, 2, and 3, respectively.
+
+\item{DONT\_MERGE\_HELICES} -- if present, the pieces of helices that contain only small breaks of hydrogen-bonding contacts (e.g., a kink) are not merged in a larger helix.
+
+\item{NLEVEL=n} -- number of classification levels.
+
+\item{n$>$0} -- the fragments for n levels will be defined manually.
+
+\item{n$<$0} -- the number of levels is -n and the fragments will be detected automatically.
+
+\item{START=n} -- the number of conformation at which to start.
+
+\item{END=n} -- the number of conformation at which to end.
+
+\item{FREQ=n} (1) - sampling frequency of conformations; e.g. FREQ=2 means that every second conformation will be considered.
+
+\item{CUTOFF\_UP=x} - upper boundary of rmsd cutoff (the value is per 50 residues).
+
+\item{CUTOFF\_LOW=x} -- lower boundary of rmsd cutoff (per 50 residues).
+
+\item{RMSUP\_LIM=x} -- lower absolute boundary of rmsd cutoff (regardless of fragment length).
+
+\item{RMSUPUP\_LIM=x} -- upper absolute boundary of rmsd cutoff (regardless of fragment length).
+
+\item{FRAC\_SEC=x} (0.66666) the fraction of native secondary structure to consider a fragment native in secondary structure.
+
+\end{description}
+
+2nd record:
+
+For nlevel$<$0 (automatic fragment assignment):
+
+\begin{description}
+
+\item{SPLIT\_BET=n} (0) : if 1, the hairpins are split into strands and strands are considered elementary fragment.
+
+\item{ANGCUT\_HEL=x} (50): cutoff on gamma angle differences from the native for a helical fragment.
+
+MAXANG\_HEL=x (60) : as above but maximum cutoff
+
+\item{ANGCUT\_BET=x} (90), MAXANG\_BET=x (360), ANGCUT\_STRAND=x (90), MAXANG\_STRAND=x (360) -- same but for a hairpin or sheet fragment.
+
+\item{FRAC\_MIN=x} (0.6666) -- minimum fraction of native secondary structure.
+
+\item{NC\_FRAC\_HEL=x (0.5)} -- fraction of native contacts for a helical fragment.
+
+\item{NC\_REQ\_HEL=x} (0) -- minimum required number of contacts.
+
+\item{NC\_FRAC\_BET=x} (0.5), NC\_REQ\_BET=x (0) -- same for beta sheet fragments.
+
+\item{NC\_FRAC\_PAIR=x} (0.3), NC\_REQ\_PAIR=x (0) : same for pairs of segments.
+
+\item{NSHIFT\_HEL=n} (3), NSHIFT\_BET=n (3), NSHIFT\_STRAND=n (3), NSHIFT\_PAIR=n (3) -- allowed sequence shift to match native and compared structure for the respective types of secondary structure.
+
+\item{RMS\_SINGLE=n} (0), CONT\_SINGLE=n (1), LOCAL\_SINGLE=n (1), RMS\_PAIR=n (0).
+
+\item{CONT\_PAIR=n} (1) -- types of criteria in considering the geometry of a fragment or pair native; 1 means that the criterion is turned on.
+
+\end{description}
+
+For nlevel$>$0 (manual assignment):
+
+Level 1:
+
+1st line:
+
+\begin{description}
+
+\item{NFRAG=n} -- number of elementary fragments.
+
+\end{description}
+
+Next lines (one group of lines per each fragment):
+
+1st line:
+
+\begin{description}
+
+\item{NPIECE=n} -- number of segments constituting the fragment.
+
+\item{ANGCUT}, MAXANG, FRAC\_MIN, NC\_FRAC, NC\_REQ -- criterial numbers of native-likeness as for automatic classification.
+
+\item{LOCAL}, ELCONT, SCCONT, RMS : types of criteria implemented, as for automatic classification except that ELECONT and SCCONT mean that electrostatic or side-chain contacts are considered, respectively.
+
+\end{description}
+
+NPIECE following lines:
+
+IFRAG1=n, IFRAG2=n -- the start and end residue of a continuous segment constituting a fragment.
+
+Level 2 and higher:
+
+1st line:
+
+\begin{description}
+
+\item{NFRAG=n} -- number of fragments considered at this level.
+
+\end{description}
+
+For each fragment the following line is read:
+
+\begin{description}
+
+\item{NPIECE=n} -- number of elementary fragments (as defined at level 1) constituting this composite fragment.
+
+\item{IPIECE=i1 i2 ... in} -- the numbers of these fragments.
+
+\item{NC\_FRAC}, NC\_REQ : contact criteria (valid only for level 2).
+
+\item{ELCONT}, SCCONT, RMS : as for level 1; note, that for level 3 and higher the only criterion of nativelikeness is rms.
+
+\end{description}
+
+3rd (for nlevel$<$0) or following (for n$>$0) line:
+
+Name of the file with reference structure (e.g., the pdb file with the experimental structure)
+
+\subsection{The structure of the main output file (out)}
+\label{sect:inoutfiles:output:main}
+
+The initial portion of the main output file, named INPUT.out\_POT\_000 contains information of parameter files specified in the C-shell script, compilation info, and the UNRES numeric code of the amino-acid sequence.
+Subsequently, actual energy-term weights and parameter files are printed. If lprint was set at .true. in parmread.F, all energy-function parameters are printed. If REFSTR was specified in the control-data list, the program then outputs the read reference-structure coordinates and partition of structure into fragments.
+Subsequently, the information about the number of structures read in and those that were rejected is printed followed by succinct information form the iteration process. Finally, the histograms (also output separately to specific histogram files; see section 6.6) and the data of the dependence of free energy, energy, heat capacity, and conformational averages on temperature are printed (these are also output separately to file described in section \ref{sect:inoutfiles:histograms}).
+
+The output files corresponding to non-master processors (INPUT.out\_POT\_xxx where xxx$>$0 contain only the information up to the iteration protocol. These files can be deleted right after the run.
+
+\subsection{The thermodynamic quantity and ensemble average (thermal) files}
+\label{sect:inoutfiles:outpput:thermo}
+
+The files INPUT.thermal or INPUT\_slice\_yy.thermal contain thermodynamic, ensemble-averaged conformation-dependent quantities and their temperature derivatives. The structure of a record is as follows:
+
+\begin{tabular}{p{2cm}p{2cm}p{2cm}p{2cm}p{2cm}p{2cm}p{2cm}}
+ T& F& E& $q_1...q_n$& rmsd& Rgy& Cv\\
+ 298.0& -83.91454& -305.28112& 0.30647& 6.28347& 11.61204&0.70886E+01\\
+\end{tabular}
+
+\begin{tabular}{p{2.5cm}p{2.5cm}p{2.5cm}p{2.5cm}p{2.5cm}p{2.5cm}}
+ $var(q_1) ...$ & var(rmsd)& var(Rgy)& $cov(q_1,E) ...$ & cov(rmsd,E)& cov(Rgy,E)\\
+ $var(q_n)$& & & $cov(q_n,E)$& & \\
+ 0.35393E-02& 0.51539E+01& 0.57012E+00& 0.43802E+00& 0.62384E+01& 0.33912E+01\\
+\end{tabular}
+
+where:
+
+\begin{description}
+
+\item{T} -- absolute temperature (in K),
+
+\item{F} -- free energy at T,
+
+\item{E} -- average energy at T,
+
+\item{$q_1..q_n$}: ensemble-averaged q values at T (usually only the total q corresponding to whole molecule is requested, as in the example above, but the user can specify more than one fragment or pair of fragments for which the q's are calculated, If there is no reference structure, this entry contains a 0,
+
+\item{rmsd} -- ensemble-averaged root mean square deviation at T,
+
+\item{Rgy} -- ensemble-averaged radius of gyration computed from Calpha coordinates at T,
+
+\item{$C_v$} -- heat capacity at T,
+
+\item{$var(q_1)...var(q_n)$} -- variances of q's at T,
+
+\item{var(rmsd)} -- variance of rmsd at T,
+
+\item{var(Rgy)} -- variance of radius of gyration at T,
+
+\item{$cov(q_1,E)...cov(q_n,E)$} -- covariances of q's and energy at T,
+
+\item{cov(rmsd,E)} -- covariance of rmsd and energy at T,
+
+\item{cov(Rgy,E)} -- covariance of radius of gyration and energy at T.
+
+\end{description}
+
+According to Camacho and Thirumalali (Europhys. Lett., 35, 627, 1996), the maximum of the variance of the radius of gyration corresponds to the collapse point of a polypeptide chain and the maximum variance of q or rmsd corresponds to the midpoint of the transition to the native structure. More precisely, these points are inflection points in the plots of the respective quantities which, with temperature-independent force field, are proportional to their covariances with energy.
+
+\subsection{The conformation summary with classification (stat) files}
+\label{sect:inoutfiles:class}
+
+The stat files (with names INPUT\_POT\_xxx.stat or INPUT\_POT\_sliceyyxxx.stat; where yy is the number of a slice and xxx is the rank of a processor) contain the output of the classification of subsequent conformations (equally partitioned between processors). The files can be concatenated by processor rank to get a summary file. Each line has the following structure (example values are also provided):
+
+
+\begin{tabular}{|c|cccc|}\hline
+&&\multicolumn{3}{c|}{whole molecule}\\
+\cline{2-5}
+No&energy&rmsd&q&ang\\ \hline
+ 9999& -122.42& 4.285&0.3751& 47.8\\ \hline
+\end{tabular}
+
+\begin{tabular}{|cccccccccccc|c|}\hline
+\multicolumn{13}{|c|}{level 1}\\ \hline
+\multicolumn{6}{|c}{frag 1}&\multicolumn{3}{c}{frag 2}&\multicolumn{3}{c|}{frag 3}&class 1\\ \cline{1-12}
+n1&n2&n3&rmsd&q&ang&rmsd&q&ang&rmsd&q&ang&\\ \hline
+ 4&10&21 & 0.6&0.33& 16.7& 3.6&0.42& 56.3& 0.7&0.12& 16.5&737 \\ \hline
+\end{tabular}
+
+\begin{tabular}{|cccccc|c|cc|c|c|} \hline
+\multicolumn{7}{|c|}{level 2}&\multicolumn{3}{c|}{level 3}&\\
+\cline{1-10}
+nc1&nc2&rmsd&q&rmsd&q&class 2&rmsd&q&class 3&class\\ \hline
+9& 0& 1.6&0.20& 4.3&0.20&20& 0& 4.0&2&737.20.2\\ \hline
+\end{tabular}
+
+% | level 1 | level 2 | level3 |
+% | | | |
+% whole mol | frag1 frag2 frag3 cl1 | | |
+%No energy rmsd q ang dif|n1n2 n3 rms q ang rms q ang rms q ang | nc1nc2 rms q rms q cl2| rms cl3|class
+% 9999 -122.42 4.285 0.3751 47.8 |4 10 21 0.6 0.33 16.7 3.6 0.42 56.3 0.7 0.12 16.5 737 | 9 0 1.6 0.20 4.3 0.20 20 | 0 4.0 2 |737.20.2
+
+where
+
+\begin{description}
+
+\item{No} -- the number of the conformation.
+
+\item{``whole molecule''} denotes the characteristics of the whole molecule q = 1-Wolynes'q.
+
+\item{level 1, 2, and 3} denote the characteristics computed for the respective fragments as these levels.
+
+\item{n1, n2, n3} -- number of native contacts for a given segment.
+
+\item{cl1, cl2, cl3} -- group of segment classes for segments at level 1, 2, and 3, respectively.
+
+\item{class} -- total class of the conformation.
+
+\end{description}
+
+The octal/quaternary/binary numbers denoting the class for a fragment at level 1, 2, and 3, respectively, are described in ref. \cite{oldziej_2004}.
+
+\subsection{The histogram files}
+\label{sect:inoutfiles:histograms}
+
+The histogram file with names INPUT\_[par\_yy][\_slice\_xx].hist where xx denotes the number of the slice and yy denotes the number of the parameter if SEPARATE\_PARSET was specified in input contain histograms of q at replica temperatures and energy-parameter sets; with SEPARATE\_PARSET histograms corresponding to subsequent parameter sets are saved in files with par\_yy infixes. The histograms are multidimensional if q is a vector (usually, however, q corresponds to the entire molecule and, consequently, the histograms are one-dimensional). The histogram files are printed if histfile and histout was specified in the control data record.
+
+Each line of a histogram file corresponds to a given (multidimensional) bin in q contains the following:
+
+
+\begin{itemize}
+
+\item
+$q_1,...,q_n$ at a given bin (format f6.3 for each)
+
+\item
+histogram values for subsequent replica temperatures (format e20.10 for each)
+
+\item
+iparm (the number of parameter set; format i5)
+
+\item
+If SEPARATE\_PARSET was not specified, the entries corresponding to each parameter follow one another.
+
+\end{itemize}
+
+The state density is printed to file(s) INPUT[\_slice\_xx].ent. Each line contains the left boundary of the energy bin and ln(state density) followed by ``ent'' string. At present, the state density is calculated correctly only if one energy-parameter set is used.</p>
+
+\subsection{The rmsd-radius of gyration potential of mean force files}
+\label{sect:inoutfiles:rmsd-rgy}
+
+These files with names INPUT[\_par\_yy][\_slice\_xx].rmsrgy contain the two-dimensional potentials of mean force in rmsd and radius of gyration at all replica-exchange temperatures and for all energy-parameter sets.
+A line contains the left boundaries of the radius of gyration -- rmsd bin (radius of gyration first) (format 2f8.2) and the PMF values at all replica-exchange temperatures (e14.5), followed by the number of the parameter set.
+With SEPARATE\_PARSET, the PMFs corresponding to different parameter sets are printed to separate files.
+
+\subsection{The PDB files}
+\label{sect:inoutfiles:PDB}
+
+The PDB files with names INPUT\_[slice\_xx\_]Tyyy.pdb, where Tyyy specifies a given replica temperature contain the conformations whose probabilities at replica temperature T sum to 0.99, after sorting the conformations
+by probabilities in descending order. The PDB files follow the standard format; see \href{ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf}{\textcolor{blue}{ftp://ftp.wwpdb.org/pub/pdb/doc/format\_descriptions}}.
+%/Format_v33_Letter.pdf">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf</a>.
+For single-chain proteins, an example is as follows:
+
+\begin{verbatim}
+REMARK CONF 9059 TEMPERATURE 330.0 RMS 8.86
+REMARK DIMENSIONLESS FREE ENERGY -1.12726E+02
+REMARK ENERGY -2.22574E+01 ENTROPY -7.87818E+01
+ATOM 1 CA VAL 1 8.480 5.714 -34.044
+ATOM 2 CB VAL 1 9.803 5.201 -33.968
+ATOM 3 CA ASP 2 8.284 2.028 -34.925
+ATOM 4 CB ASP 2 7.460 0.983 -33.832
+.
+.
+.
+ATOM 115 CA LYS 58 28.446 -3.448 -12.936
+ATOM 116 CB LYS 58 26.613 -4.175 -14.514
+TER
+CONECT 1 3 2
+.
+.
+.
+CONECT 113 115 114
+CONECT 115 116
+\end{verbatim}
+
+where
+
+\begin{description}
+
+\item{CONF} is the number of the conformation from the processed slice of MREMD trajectories.
+
+\item{TEMPERATURE} is the replica temperature.
+
+\item{RMS} is the Calpha rmsd from the reference (experimental) structure.
+
+\item{DIMENSIONLESS FREE ENERGY} is -log(probability) (equation 14 of ref 2) for the conformation at this replica temperature calculated by WHAM.
+
+\item{ENERGY} is the UNRES energy of the conformation at the replica temperature (note that UNRES energy is in general temperature dependent).
+
+\item{ENTROPY} is the omega of equation 15 of ref 2 of the conformation.
+
+\end{description}
+
+In the ATOM entries, CA denotes a Calpha atom and CB denotes UNRES side-chain atom. The CONECT entries specify the C$^\alpha_i\cdots$C$^\alpha_{i-1}$, C$^\alpha_i\cdots$C$^\alpha_{i+1}$ and C$^\alpha_i\cdots$SC$_i$ links.
+
+The PDB files generated for oligomeric proteins are similar except that chains are separated with TER and molecules with ENDMDL records and chain identifiers are included. An example is as follows:
+
+\begin{verbatim}
+REMARK CONF 765 TEMPERATURE 301.0 RMS 11.89
+REMARK DIMENSIONLESS FREE ENERGY -4.48514E+02
+REMARK ENERGY -3.58633E+02 ENTROPY 1.51120E+02
+ATOM 1 CA GLY A 1 -0.736 11.305 24.600
+ATOM 2 CA TYR A 2 -3.184 9.928 21.998
+ATOM 3 CB TYR A 2 -1.474 10.815 20.433
+.
+.
+.
+ATOM 40 CB MET A 21 -4.033 -2.913 27.189
+ATOM 41 CA GLY A 22 -5.795 -10.240 27.249
+TER
+ATOM 42 CA GLY B 1 6.750 -6.905 19.263
+ATOM 43 CA TYR B 2 5.667 -4.681 16.362
+.
+.
+.
+ATOM 163 CB MET D 21 4.439 12.326 -4.950
+ATOM 164 CA GLY D 22 10.096 14.370 -9.301
+TER
+CONECT 1 2
+CONECT 2 4 3
+.
+.
+.
+CONECT 39 41 40
+CONECT 42 43
+.
+.
+.
+CONECT 162 164 163
+ENDMDL
+\end{verbatim}
+
+\subsection{The compressed Cartesian coordinates (cx) files}
+\label{sect:inoutfiles:cx}
+
+These files contain compressed data in the Europort Data Compression XDRF library format written by Dr. F. van Hoesel, Groeningen University (\href{http://hpcv100.rc.rug.nl/xdrfman.html}{http://hpcv100.rc.rug.nl/xdrfman.html}.
+The files are written by the cxwrite subroutine. The resulting cx file contains the omega factors to compute probabilities of conformations at any temperature and any energy-function parameters if Hamiltonian replica
+exchange was performed in the preceding UNRES run. The files have general names INPUT[\_par\_yy][\_slice\_xx].cx where xx is slice number and yy is parameter-set.
+
+The items written to the cx file are as follows (the precision is 5 significant digits):
+
+\begin{enumerate}
+\item
+Cartesian coordinates of Calpha and SC sites</p>
+\item
+nss (number of disulfide bonds)
+\item
+if nss$>$0:
+\begin{enumerate}
+\item
+ihpb (first residue of a disulfide link)
+\item
+jhpb (second residue of a disulfide link)
+\item
+UNRES energy at that replica temperature that the conformation was at snapshot-recording time,
+\item
+ln(omega) of eq 15 of ref \cite{liwo_2007},
+\end{enumerate}
+\item
+C$^\alpha$ rmsd
+\item
+conformation class number (0 if CLASSIFY was not specified).
+\end{enumerate}
+
+\newpage
+
+\section{SUPPORT}
+\label{sect:support}
+
+ Dr. Adam Liwo\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ phone: +48 58 523 5124\\
+ fax: +48 58 523 5012\\
+ e-mail: \href{mailto:adam@sun1.chem.univ.gda.pl}{\textcolor{blue}{adam@sun1.chem.univ.gda.pl}}\\
+
+ Dr. Cezary Czaplewski\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ phone: +48 58 523 5126\\
+ fax: +48 58 523 5012\\
+ e-mail: \href{mailto:cezary.czaplewski@ug.edu.pl}{\textcolor{blue}{cezary.czaplewski@ug.edu.pl}}\\
+\\
+
+ Dr. Adam Sieradzan\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ phone: +48 58 523 5124\\
+ fax: +48 58 523 5012\\
+ e-mail: \href{mailto:adasko@sun1.chem.univ.gda.pl}{\textcolor{blue}{adasko@sun1.chem.univ.gda.pl}}\\
+
+Prepared by Adam Liwo, 02/19/12.
+
+\LaTeX version, 09/27/12.
+
+Revised by Adam Liwo, 12/04/14
+
+\end{document}
projects / unres.git / commitdiff